Proteopedia - User contributions [en]

File:028 pot.mrc

2026-10-07T16:36:06Z

Jaime Prilusky:

User:Jaime Prilusky/Test/Dummy page

2026-10-05T08:03:46Z

Jaime Prilusky:

==The discovery of glycine and related amino acid-based factor xa inhibitors==
<StructureSection viewer='molstar' load='2q1j' size='340' side='right'caption='[[2q1j]], [[Resolution|resolution]] 1.90Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2q1j]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q1J FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=FXI:1-(BUTYL{[(4-CHLOROPHENYL)AMINO]CARBONYL}AMINO)-N-[3-FLUORO-2-(METHYLSULFONYL)BIPHENYL-4-YL]CYCLOPROPANECARBOXAMIDE'>FXI</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q1j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1j OCA], [https://pdbe.org/2q1j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q1j RCSB], [https://www.ebi.ac.uk/pdbsum/2q1j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q1j ProSAT]</span></td></tr>
</table>
== Disease ==
[https://www.uniprot.org/uniprot/FA10_HUMAN FA10_HUMAN] Defects in F10 are the cause of factor X deficiency (FA10D) [MIM:[https://omim.org/entry/227600 227600]. A hemorrhagic disease with variable presentation. Affected individuals can manifest prolonged nasal and mucosal hemorrhage, menorrhagia, hematuria, and occasionally hemarthrosis. Some patients do not have clinical bleeding diathesis.<ref>PMID:2790181</ref> <ref>PMID:1973167</ref> <ref>PMID:1985698</ref> <ref>PMID:7669671</ref> <ref>PMID:8529633</ref> <ref>PMID:7860069</ref> <ref>PMID:8845463</ref> <ref>PMID:8910490</ref> <ref>PMID:10468877</ref> <ref>PMID:10746568</ref> <ref>PMID:10739379</ref> <ref>PMID:11248282</ref> <ref>PMID:11728527</ref> <ref>PMID:12945883</ref> <ref>PMID:15650540</ref> <ref>PMID:17393015</ref> <ref>PMID:19135706</ref>
== Function ==
[https://www.uniprot.org/uniprot/FA10_HUMAN FA10_HUMAN] Factor Xa is a vitamin K-dependent glycoprotein that converts prothrombin to thrombin in the presence of factor Va, calcium and phospholipid during blood clotting.
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
<jmolCheckbox>
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q1/2q1j_consurf.spt"</scriptWhenChecked>
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
<text>to colour the structure by Evolutionary Conservation</text>
</jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2q1j ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Herein, we report on the identification of three potent glycine and related amino acid-based series of FXa inhibitors containing a neutral P1 chlorophenyl pharmacophore. A X-ray crystal structure has shown that constrained glycine derivatives with optimized N-substitution can greatly increase hydrophobic interactions in the FXa active site. Also, the substitution of a pyridone ring for a phenylsulfone ring in the P4 sidechain resulted in an inhibitor with enhanced oral bioavailability.

The discovery of glycine and related amino acid-based factor Xa inhibitors.,Kohrt JT, Filipski KJ, Cody WL, Bigge CF, La F, Welch K, Dahring T, Bryant JW, Leonard D, Bolton G, Narasimhan L, Zhang E, Peterson JT, Haarer S, Sahasrabudhe V, Janiczek N, Desiraju S, Hena M, Fiakpui C, Saraswat N, Sharma R, Sun S, Maiti SN, Leadley R, Edmunds JJ Bioorg Med Chem. 2006 Jul 1;14(13):4379-92. Epub 2006 Mar 10. PMID:16529937<ref>PMID:16529937</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2q1j" style="background-color:#fffaf0;"></div>

==See Also==
*[[Factor Xa|Factor Xa]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Bigge CF]]
[[Category: Cody WL]]
[[Category: Filipski KJ]]
[[Category: Finzel BC]]
[[Category: Kohrt JT]]
[[Category: Zhang E]]

Regulator of G protein signaling

2026-10-04T14:14:23Z

Jaime Prilusky:

==Regulator of G protein signaling (RGS) interactions with G proteins – RGS4-Gα<sub>i</sub> as a model structure.==
<StructureSection load='' size='340' side='right' caption='Rat regulator of G-protein signalling 4 (red) complex with guanine nucleotide-binding protein α subunit (grey) (PDB id [[1agr]])' scene='70/701447/Gi-rgs4/9' pspeed='8'>
== Heterotrimeric G-proteins family ==
Human heterotrimeric G-proteins are derived from 35 genes: 16 encoding α subunits, 5 β and 14 γ subunits.
The α subunits function as guanine nucleotide on-off switches, mechanistically similar to other G-proteins that are enzymatic GTPases.
G-proteins interact with diverse protein partners, such as G-protein coupled receptors (GPCRs), downstream effectors, and other proteins.
One important G-protein interaction is with members of the RGS protein family. This interaction occurs when the G-protein alpha subunit is activated, and depends on the Gα class, which in turn depends on their sequence that classifies them into several sub-types. Based on the Phylogenetic tree of mammalian G-protein, G-protein α-subunits are classified to 4 groups based on their sequence identity. The first two groups, Gα<sub>i</sub> and Gα<sub>q</sub> families have selectivity towards The RGS members of R4-subfamily and R12-subfamily. Another group, Gα<sub>z</sub> subunits were suggested to have selectivity for the RGS members of RZ-subfamily. The last subfamilies Gα<sub>s</sub> and Gα<sub>12/13</sub> might interact with diverse proteins subfamilies that include the ~120-residue RGS homology domain but can't interact with canonical RGS members.

[[Image:Ga_family_figure1-heterotrimeric_G-protein-short_history_06.jpg|300px|Homology of mammalian G-protein α-subunits.]]

Phylogenetic tree of mammalian G-protein α-subunits classified to 4 groups based on their sequence identity.<ref name="Milligan2006">PMID: 16402120</ref>

== RGS proteins ==
'''Regulator of G-proteins signaling''' (RGS) proteins play a critical role in many G protein-dependent signaling pathways. Thus, RGS proteins have been implicated in a wide range of pathologies, including cancer, hypertension, arrhythmias, drug abuse and schizophrenia. RGS proteins ‘turn off’ heterotrimeric (αβγ) G-proteins and thereby determine the duration of G protein–mediated signaling events. Therefore, RGS proteins function as GTPase Activating Proteins (GAPs), and this GAP activity is mediated by allosteric interactions.
RGS proteins are selective for binding to the transition state of Gα(GTP → GDP + P<sub>i</sub>).

Like many signaling proteins, RGS proteins comprise a large and diverse family. In human genome, Thirty-seven RGS proteins are encoded by gene loci; this collection of related proteins has been divided into 10 different subfamilies based on the relatedness of their RGS domain sequence and their multiple domain architectures. The major subfamily contains About 20 ‘canonical’ RGS proteins that can in theory downregulate any of the 16 activated Gα subunits, although in practice they interact only with members of the G<sub>i</sub> and G<sub>q</sub> families. In these proteins, the ~120-residue RGS homology domain functions as a GTPase-activating protein (GAP) for GTP-bound Gα subunits. In addition to these domains, diverse proteins subfamilies include additional protein-protein interaction domains beyond their signature RGS domain with Gα GAP activity. R7-subfamily members share a multi-domain protein architecture composed of DEP and GGL domains on the N-terminal side of the RGS domain. R12-subfamily members possess a tandem repeat of Ras binding domains (RBDs) and a single GoLoco motif.

[[Image:Kosloff-NSMB2011-Fig1b.jpg|350px|family of canonical RGS proteins]]

Phylogenetic tree of 19 human RGS domains.
RGS proteins whose activity was tested are colored by their GAP activity, RGS proteins with high GAP activity (green), RGS proteins with low but discernible activities (purple) and RGS2 had no measurable activity (red).
<ref name="Mickey2011">PMID: 21685921</ref>

== Various RGSs and their functions ==

*'''RGS1''' selectively regulates gut T cell trafficking and colitis potential<ref>PMID:21795595</ref>.<br />
*'''RGS2''' regulates airway hyper responsiveness related to asthma<ref>PMID:25368964</ref>.<br />
*'''RGS3''' is associated with glioma cell motility<ref>PMID:15055445</ref>.<br />
*'''RGS4''' is associated with schizophrenia<ref>PMID:15274033</ref>.<br />
*'''RGS5''' controls blood pressure homeostasis<ref>PMID:23303165</ref>.<br />
*'''RGS6''' promotes anxiety and depression<ref>PMID:24421401</ref>.<br />
*'''RGS9-1''' mediates G protein function in photoreceptors<ref>PMID:11601986</ref>.<br />
*'''RGS10''' negatively regulates cardia remodeling<ref>PMID:26573707</ref>.<br />
*'''RGS12''' regulates osteoclast differentiation<ref>PMID:25909889</ref>.<br />
*'''RGS14''' is an selective Hras effector <ref>PMID:19319189</ref>.<br />
*'''RGS16''' inhibits hepatic fatty acid oxidation<ref>PMID:21357625</ref>.<br />
*'''RGS17''' is a negative modulator of G protein-coupled receptor signaling in human cancers<ref>PMID:26928451</ref>.<br />
*'''RGS18''' regulates platelet aggregation and thrombosis<ref>PMID:25969426</ref>.<br />

== RGS4 Structural highlights ==
Structure [[1agr]] is a complex of RGS4 and Gα<sub>i1</sub> proteins defined by X-ray crystallographic analysis.
<scene name='70/701447/Rgs4_monomer/10'> The RGS4 domain </scene> corresponds to an array of nine α-helices: α1, α2, α3, α4, α5 and α6 helices are colored in blue, aqua, yellow, coral, magenta and dark green respectively, while helices α7, α8 and α9 are colored red. The 3D structure of RGS4 protein fold into <scene name='70/701447/Rgs4_subdomains/5'>two small subdomains</scene>, the terminal subdomain colored magenta, contains the N and C termini of the box and is formed by α1, α2, α3, α8, and α9; and the larger bundle subdomain colored cyan formed by α4, α5, α6, and α7. The both two subdomains are required for RGS4 GAP activity.

== Gα<sub>i1</sub> Structural highlights ==
Gα<sub>i1</sub> subunits adopt a conserved fold of <scene name='70/701447/All-helical-domain/7'>α helical domain</scene> that composed of six α helices shown as blue cartoon, and a conserved GTPase domain shown in gray cartoon. The GTPase domain hydrolyzes GTP and provides most of Gα's binding surfaces for Gβγ, receptors, effectors and RGS proteins. <scene name='70/701447/Gi-rgs4/22'>The GTPase domain</scene> contains three flexible regions designated switch-I presented as blue sticks, switch-II presented as magenta sticks and switch-III presented as green sticks that change conformation in response to GTP binding and hydrolysis, GDP–Mg<sup>+2</sup> bound in the active site of Gα<sub>i1</sub> is shown as a ball-and-stick model. The three switch regions of Gα<sub>i1</sub> residues: 176–184, 201–215, and 233–241, respectively. <ref name="Tesmer97">PMID: 9108480</ref>

== RGS-G proteins interactions ==
Many RGS protein residues located in the vicinity of the <scene name='70/701447/Rgs4-ga_interface/4'>RGS domain–Gα interface</scene> (RGS protein shown as wheat cartoon and Gα<sub>i1</sub> subunit shown as white surface) contribute to RGS-G proteins interaction. Based on energy calculation and experimental validation of RGS-Gα complexes from Gα<sub>i</sub> subfamily members, these residues classified into two major groups: <scene name='70/701447/Rgs4-ga-sandc-residues/4'>Significant and Conserved residues</scene> shown as red spheres that are located mainly in the center of the RGS domain–Gα interface and have a primary role in accelerating Gα GTPase by stabilizing Gα in an optimal conformation for GTP hydrolysis. Whereas the <scene name='70/701447/Rgs4-ga_modulatory_residues/2'>putative Modulatory residues</scene> shown as purple spheres are located mostly at the periphery of the interface where they contribute to Gα subunit's recognition.<ref name="Mickey2011" />

On the other side, Gα subunits participate in a range of interactions with a variety of other proteins. Therefore, they have interfaces that interact selectively with receptors, effector subfamilies and RGS proteins. However, <scene name='70/701447/Gi-rgs4_interface/4'>Gα residues</scene> from Gα<sub>i</sub> subfamily members that interact specifically with RGS proteins are highly conserved (red spheres). These Gα Residues located on Gα switch regions interact with Significant & Conserved RGS residues because of the pivotal role of the switch regions in GTP hydrolysis that is catalyzed by RGS proteins. On the other hand, Gα residues located in switch regions II and III and multiple residues in the Gα all-helical domain interact with Modulatory RGS residues.<ref name="Mickey2011" /> For example, one important conserved RGS4 residue that projects into the active site of Gα<sub>i</sub> is <scene name='70/701447/Gi-rgs4-asn128/2'>Asn-128</scene> shown as blue sticks, which contacts the side chains of three Gα residues: Lys-180, Gln-204, and Glu-207 shown as green, magenta, and red sticks respectively.<ref name="Tesmer97" /> A unique modulatory RGS4 residue that interacts with Gα<sub>i</sub> is <scene name='70/701447/Gi-rgs4_arg166/6'>Arg-166</scene> shown as blue sticks which forms salt bridge with the positively charged side chain of Glu-116 shown as magenta sticks located in the helical domain of Gα subunit.

==3D structures of regulator of G-protein signaling==
[[Regulator of G-protein signaling 3D structures]]

</StructureSection>

== References ==

<references/>
[[Category:Topic Page]]

Regulator of G-protein signaling 3D structures

2026-10-04T14:04:23Z

Jaime Prilusky: Jaime Prilusky moved page Regulator of G-protein signaling 3D structures to Regulator of G protein signaling 3D structures: removed extra hyphen on name

#REDIRECT [[Regulator of G protein signaling 3D structures]]

Regulator of G protein signaling 3D structures

2026-10-04T14:04:22Z

Jaime Prilusky: Jaime Prilusky moved page Regulator of G-protein signaling 3D structures to Regulator of G protein signaling 3D structures: removed extra hyphen on name

==3D structures of regulator of G-protein signaling==
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|

* Regulator of G-protein signaling 1

**[[2bv1]] – hRGS1 – human<br />
**[[2gtp]] – hRGS1 + guanine nucleotide-binding protein subunit α1 <br />
**[[4pni]] – bRGS1 – bovine<br />

* Regulator of G-protein signaling 2

**[[2af0]] – hRGS2<br />
**[[4ekc]], [[4ekd]] – hRGS2 + guanine nucleotide-binding protein subunit α <br />
**[[2v4z]] – hRGS2 (mutant) + guanine nucleotide-binding protein subunit α <br />
**[[3v5w]] – hRGS2 + guanine nucleotide-binding protein subunit β1 and γ2 <br />

* Regulator of G-protein signaling 3

**[[2f5y]] – hRGS3 PDZ domain 15-183<br />
**[[2oj4]] – hRGS3<br />
**[[3fbk]] – hRGS3 C2 domain 134-276<br />
**[[1whd]] – mRGS3 PDZ domain - mouse<br />

* Regulator of G-protein signaling 4

**[[1agr]] – rRGS4 + guanine nucleotide-binding protein subunit α – rat <br />
**[[1ezt]], [[1ezy]] – rRGS4 - NMR<br />

* Regulator of G-protein signaling 5

**[[2crp]] – hRGS5 - NMR<br />

* Regulator of G-protein signaling 6

**[[2es0]] – hRGS6<br />

* Regulator of G-protein signaling 7

**[[2a72]] – hRGS7<br />
**[[2d9j]] – hRGS7 - NMR<br />
**[[7ewp]], [[7ewr]], [[7shf]] – hRGS7 + guanine nucleotide-binding protein subunit ab-5 + GPR158 – Cryo EM<br />
**[[9vos]] – hRGS7 + guanine nucleotide-binding protein subunit ab-5 + MGlyR + nanobody – Cryo EM<br />

* Regulator of G-protein signaling 8

**[[2ihd]] – hRGS8<br />
**[[2ode]] – hRGS8 + guanine nucleotide-binding protein subunit α <br />
**[[5do9]] – mRGS8 + guanine nucleotide-binding protein subunit α <br />

* Regulator of G-protein signaling 9

**[[1fqi]] – bRGS9<br />
**[[1fqj]] – bRGS9 + guanine nucleotide-binding protein subunit α + phosphodiesterase subunit γ <br />
**[[1fqk]] – bRGS9 + guanine nucleotide-binding protein subunit α <br />
**[[2pbi]] – mRGS9 + guanine nucleotide-binding protein subunit β5 <br />

* Regulator of G-protein signaling 10

**[[2i59]], [[2dlr]] – hRGS10 - NMR<br />
**[[2ihb]] – hRGS10 + guanine nucleotide-binding protein subunit α <br />

* Regulator of G-protein signaling 12

**[[2ebz]] – hRGS12 RGS domain - NMR <br />
**[[2kv8]] - hRGS12 PDZ domain 18-100 - NMR<br />

* Regulator of G-protein signaling 14

**[[2om2]], [[3onw]] – hRGS14 GOLOCO motif + guanine nucleotide-binding protein subunit α <br />
**[[2jnu]] – hRGS14 - NMR <br />
**[[1wfy]] - mRGS14 Ras-binding domain - NMR<br />

* Regulator of G-protein signaling 16

**[[2bt2]] – hRGS16<br />
**[[3c7k]], [[3c7l]], [[2ik8]] – hRGS16 + guanine nucleotide-binding protein subunit α <br />

* Regulator of G-protein signaling 17

**[[1zv4]], [[6am3]] – hRGS17<br />
**[[6n9g]] – bRGS17 + guanine nucleotide-binding protein subunit β-5 <br />

* Regulator of G-protein signaling 18

**[[2dlv]], [[2owi]], [[2jm5]] – hRGS18 - NMR <br />
}}

[[Category:Topic Page]]

Recoverin, a calcium-activated myristoyl switch

2026-10-04T09:29:53Z

Jaime Prilusky: Jaime Prilusky moved page Recoverin, a calcium-activated myristoyl switch to Recoverin over redirect: bad name

#REDIRECT [[Recoverin]]

Recoverin

2026-10-04T09:29:53Z

Jaime Prilusky: Jaime Prilusky moved page Recoverin, a calcium-activated myristoyl switch to Recoverin over redirect: bad name

<StructureSection load='' size='350' side='right' scene='Recoverin,_a_calcium-activated_myristoyl_switch/Recoverin_morph/2' caption='Recoverin: [[1iku]] model 7 (calcium-free) morphed to [[1jsa]] model 9 (calcium-bound) complex with myristic acid.' >

==Function==

'''Recoverin''' is a 23 kD protein that regulates recovery of the eye from exposure to light, and the adaptation to background light. Recoverin controls the lifetime of photoactivated rhodopsin. Recoverin in turn is regulated by calcium ions, which cause recoverin molecules to associate with the disc membranes which fill the photosensitive portion of the rod cells in the eye, rather than diffusing freely in the cytosol.

==Myristoyl Switch and Calcium==
<scene name='Recoverin,_a_calcium-activated_myristoyl_switch/Recoverin_no_calcium/2'>Recoverin</scene> (Initial colors: '''<font color="#808080">Hydrophobic</font>, <font color="#e000e0">Polar</font>''') has a <scene name='Recoverin,_a_calcium-activated_myristoyl_switch/Recoverin_morph/5'>myristic acid</scene> (14-carbon saturated fatty acid, or a similar acyl moiety) covalently linked via an amide bond to its N-terminal glycine. In the absence of calcium, the <scene name='Recoverin,_a_calcium-activated_myristoyl_switch/Recoverin_no_calcium/1'>myristoyl group is buried</scene> in the N-terminal protein domain, surrounded on all sides by alpha helices that form a hydrophobic pocket. The binding of <scene name='Recoverin,_a_calcium-activated_myristoyl_switch/Recoverin_morph/6'>two calcium ions</scene> to each recoverin molecule induces a <scene name='Recoverin,_a_calcium-activated_myristoyl_switch/Recoverin_morph/1'>conformational change </scene> that extrudes the myristoyl and exposes some hydrophobic amino acids on the surface. This enables the molecule to bind to the lipid bilayers of the disc membranes. <scene name='24/241531/Recoverin_storymorph/1'>An alternate morph</scene> <ref>The [[Jmol/Storymorph|Storymorph Jmol scripts]] were used to create the interpolation shown in the morph. [https://proteopedia.org/wiki/index.php/Image:Morph_recoverin.pdb Coordinates] available on Proteopedia</ref> emphasizes that two parts of the molecule rotate relative to each other while retaining their local fold.

{{Template:Button Toggle Animation2}}

The two calcium ions each bind to an EF hand motif, one in the C-terminal domain, and one in the N-terminal domain. Recoverin actually contains four EF hand motifs, but two of them are unable to bind calcium due to variations in sequence.

Recoverin, which has been described as a calcium-myristoyl switch, is a member of a large family of sequence-similar proteins found from yeast through invertebrates and mammals. Those found in the nervous system are suspected to "participate in membrane-associated signal transduction processes by coupling G-protein receptors to calcium cascades" (Tanaka et al., 1995<ref name="tanaka1995">Tanaka T, Ames JB, Harvey TS, Stryer L, Ikura M, Nature 376(6539):444-447, 1995. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7630423 7630423]</ref>).

==3D Structure==

Recoverin was the first member of the calcium-myristoyl switch family family whose 3D structure was determined. The structure of the calcium-free form was determined by solution NMR in 1995<ref name="tanaka1995"/>. Determination of the calcium-bound, hydrophobic form by solution NMR required modification of the myristoyl: carbon in the 13th position was replaced with oxygen (Ames et al., 1997<ref>Ames JB, Ishima R, Tanaka T, Gordon JI, Stryer L, Ikura M, Nature 389(6647):198-202, 1997. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9296500 9296500]</ref>). The 13-oxa myristoyl analog recoverin retains a functional calcium-myristoyl switch, and the calcium-bound conformation is very similar to the natural form (by heteronuclear single quantum coherence spectra).

The [[Morphs]] provided here illustrate the structural relationships between the calcium-free, water-soluble conformation, and the calcium-bound, hydrophobic conformation.

==Technical Notes==
Both [[1iku]] and [[1jsa]] are ensembles of NMR models. The morph is a [[Morphs |linear interpolation morph]] between model 7 and model 9, respectively. Only the alpha carbon atoms of the protein are present in the morph PDB file. For the space-filled model 7 of 1iku, hydrogen atoms were deleted except for those in the myristoyl adduct. The alternate morph preserving rigid domains was created using the [[Jmol/Storymorph|Storymorph Jmol scripts]].
</StructureSection>
__NOTOC__
==3D structures of recoverin ==

Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}

[[2d8n]] – RCV – human<br />
[[2het]], [[1omr]], [[1rec]], [[4m2q]], [[4mlw]] – bRCV – bovine<br />
[[1jsa]], [[1iku]] - bRCV - NMR<br />
[[1omv]], [[4m2o]], [[4m2p]], [[4yi8]], [[4yi9]] – bRCV (mutant)<br />
[[1la3]] - bRCV (mutant) - NMR<br />
[[2i94]] – bRCV + rhodopsin kinase

==Credits==
This page was adapted from ''The Protein Morpher'', a defunct, Chime-based website written in 1998 by Eric Martz.

==References==

<references/>

See Also:

*[http://structbio.vanderbilt.edu/cabp_database/general/prot_pages/recov.html Recoverin] in the [http://www.structbio.vanderbilt.edu/cabp_database/ The EF-Hand Calcium-Binding Proteins Data Library].

[[Category:Topic Page]]

Recombinase A

2026-10-04T09:05:25Z

Jaime Prilusky:

<StructureSection load='2REB' size='350' side='right' scene='' caption='E.coli RecA (PDB code [[2reb]])'>

== Function ==
[[Recombinase A]] (RecA), a naturally aggregating protein involved in DNA repair, is an important asset to the genetic integrity of the ''Escherichia coli'' (''E. coli'') genome.<ref name=Shan> Shan, Q.; Cox, M. M.; Inman, R. B. DNA Strand Exchange Promoted by RecA K72R. J. Biol. Chem. 1996, 271, 5712-5724. DOI:10.1074/jbc.271.10.5712 </ref> The survival of all species rely on such DNA repair processes. RecA homologues are found in all kingdoms including archaebacteria, eubacteria, and eukaryotes.<ref name=Brendel> Brendel, V.; Brocchieri, L.; Sandler, S.J.; Clark, A.J.; Karlin, S. Evolutionary comparisons of RecA-like proteins across all major kingdoms of living organisms. J. Mol. Evol. 1997, 44, 528-541. DOI: 10.1007/PL00006177 </ref> Rad51, for example, is a RecA homologue found specifically in humans.<ref name=Baumann> Baumann, P.; Benson, F. E.; West, S. C. Human Rad51 Protein Promotes ATP-Dependent Homologous Pairing and Strand Transfer Reactions in Vitro. Cell. 1996, 87, 757-766. DOI: 10.1016/S0092-8674(00)81394-X </ref> An over-expression of Rad51 in the nuclei of tumor cells when compared to those of normal breast tissue has been linked to sporadic, non-hereditary, breast cancers.<ref name=Maacke> Maacke, H.; Opitz, S.; Jost, K.; Hamdorf, W.; Henning, W. Krüger, S. Feller, A.C.; Lopens, A.; Diedrich, K.; Schwinger, E.; Stürzbecher, H.W. Over-expression of wild-type Rad51 correlates with histological grading of invasive ductal breast cancer. Int. J. Cancer. 2000, 88, 907-913. DOI: 10.1002/1097-0215(20001215)88:63.0.CO;2-4 </ref> See also [[Isomerases]], [[DNA Repair]].

== DNA Repair ==
In ''E. coli'', RecA’s central function involves strand exchange, specifically recombinational DNA repair.<ref name=Roca> Roca, A. I.; Cox, M. M. RecA Protein: Structure, Function, and Role in Recombinational DNA Repair. Prog. Nucleic Acid Res. Mol. Biol. 1997, 56, 129-223. DOI: 10.1016/S0079-6603(08)61005-3 </ref> The DNA recombination mechanism for RecA is a process that results in the exchange of strands between two homologous DNA molecules.<ref name=Nayak> Nayak, S.; Hildebrand, E.L.; Bryant, F.R. ADP-dependent DNA strand exchange by the Mutant RecA protein. J. Biol. Chem.2001, 276, 14933-14938. DOI:10.1074/jbc.M100470200 </ref> The DNA that results from this process is a nicked circular dsDNA molecule and one or two linear ssDNA molecules, depending on the number of DNA strands involved (three or four).<ref name=Roca> Roca, A. I.; Cox, M. M. RecA Protein: Structure, Function, and Role in Recombinational DNA Repair. Prog. Nucleic Acid Res. Mol. Biol. 1997, 56, 129-223. DOI: 10.1016/S0079-6603(08)61005-3 </ref> <ref name=Nayak> Nayak, S.; Hildebrand, E.L.; Bryant, F.R. ADP-dependent DNA strand exchange by the Mutant RecA protein. J. Biol. Chem.2001, 276, 14933-14938. DOI:10.1074/jbc.M100470200 </ref> During DNA strand exchange, adenosine triphosphate (ATP) is hydrolyzed to form adenosine diphosphate (ADP) and inorganic phosphate (Pi). ATP hydrolysis is required for DNA strand exchange to be unidirectional (without ATP hydrolysis, strand exchange is also bidirectional), for the circumvention of various structural obstacles on the DNA molecule such as heterologous inserts, and for DNA strand exchange to occur with four stands of DNA.<ref name=Shan> Shan, Q.; Cox, M. M.; Inman, R. B. DNA Strand Exchange Promoted by RecA K72R. J. Biol. Chem. 1996, 271, 5712-5724. DOI:10.1074/jbc.271.10.5712 </ref> <ref name=Roca> Roca, A. I.; Cox, M. M. RecA Protein: Structure, Function, and Role in Recombinational DNA Repair. Prog. Nucleic Acid Res. Mol. Biol. 1997, 56, 129-223. DOI: 10.1016/S0079-6603(08)61005-3 </ref>

== Other RecA Functions ==
RecA is also involved in inducing the SOS response to DNA damage by assisting in the cleavage, and consequent inactivation, of proteins.<ref name=Roca> Roca, A. I.; Cox, M. M. RecA Protein: Structure, Function, and Role in Recombinational DNA Repair. Prog. Nucleic Acid Res. Mol. Biol. 1997, 56, 129-223. DOI: 10.1016/S0079-6603(08)61005-3 </ref> Examples of such proteins are the LexA repressor and the λ repressor.<ref name=Roca> Roca, A. I.; Cox, M. M. RecA Protein: Structure, Function, and Role in Recombinational DNA Repair. Prog. Nucleic Acid Res. Mol. Biol. 1997, 56, 129-223. DOI: 10.1016/S0079-6603(08)61005-3 </ref>

== Binding Sites on RecA ==
As RecA has many different functions, it also has several different <scene name='41/413118/Reca_adp_mg/3'>binding sites</scene> (ADP in Orange/Red and Mg ion in lime green) for DNA, ADP, ATP, the LexA repressor, the λ repressor, as well as other RecA protein monomers to form a variety of oligomers.<ref name=Roca> Roca, A. I.; Cox, M. M. RecA Protein: Structure, Function, and Role in Recombinational DNA Repair. Prog. Nucleic Acid Res. Mol. Biol. 1997, 56, 129-223. DOI: 10.1016/S0079-6603(08)61005-3 </ref> <ref name=Story> Story, R. M.; Weber, I. T.; Steitz, T. A. The structure of the E. coli recA protein monomer and polymer. Nature (London) 1992, 355, 318-325. DOI: 10.1038/355318a0 </ref> <ref name=Walker> Walker, J. E.; Saraste, M.; Runswick, M. J. Gay, N. J. Distantly related sequences in the α- and β-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1982, 1, 945-951. PMCID: PMC553140 </ref> The <scene name='41/413118/Reca_filament_dna_bound/1'>RecA helical filament</scene> (single-stranded DNA colored purple, ATP colored magenta, and Aluminum tetrafluoride colored lime green) consists of six RecA monomers per turn of the helix, and each individual monomer is capable of binding three base pairs of the extended conformation of DNA.<ref name=Cox> Cox, M. M. Motoring along with the bacterial RecA protein. Nat. Rev. Mol. Cell Biol. 2007, 8, 127-138. DOI: 10.1038/nrm2099 </ref> This filament is not the only oligomer of RecA that exists in solution, however. Sattin and Goh have reported a variety of RecA structures in buffer, such as monomers, hexamers, rods/fibrils, protofibrils, and other small aggregates.<ref name=Sattin> Sattin, B. D.; Goh, M. C. Novel polymorphism of recA fibrils revealed by Atomic Force Microscopy. J. Biol. Phys. 2006, 32, 153-168. DOI: 10.1007/s10867-006-9010-3 </ref> Moreover, the type and amount of these different aggregation states is dynamic. Brenner and Zlotnick reported that the presence of monovalent salts changed the distribution of RecA aggregation states and that higher protein concentration tended to correspond to more aggregated structures.<ref name=Brenner> Brenner, S. L.; Zlotnick, A. RecA Protein Self-assembly: Multiple Discrete Aggregation States. J. Mol. Biol. 1988, 204, 959-972. DOI: 10.1016/0022-2836(88)90055-1 </ref> ATP hydrolysis occurs in the region of a loop consisting of amino acids 66-73 of the protein, which corresponds to the Walker A box motif and has the sequence GPESSGKT.<ref name=Roca> Roca, A. I.; Cox, M. M. RecA Protein: Structure, Function, and Role in Recombinational DNA Repair. Prog. Nucleic Acid Res. Mol. Biol. 1997, 56, 129-223. DOI: 10.1016/S0079-6603(08)61005-3 </ref> <ref name=Story> Story, R. M.; Weber, I. T.; Steitz, T. A. The structure of the E. coli recA protein monomer and polymer. Nature (London) 1992, 355, 318-325. DOI: 10.1038/355318a0 </ref> This sequence corresponds to a variation known as the <scene name='41/413118/1/1'>phosphate binding loop</scene> (phosphate ion shown in Red/Orange), which has a sequence [G/A]XXXXGK[T/S] found in many nucleoside triphosphate (NTP)-binding proteins.<ref name=Story> Story, R. M.; Weber, I. T.; Steitz, T. A. The structure of the E. coli recA protein monomer and polymer. Nature (London) 1992, 355, 318-325. DOI: 10.1038/355318a0 </ref> <ref name=Walker> Walker, J. E.; Saraste, M.; Runswick, M. J. Gay, N. J. Distantly related sequences in the α- and β-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1982, 1, 945-951. PMCID: PMC553140 </ref> Several of the residues in this phosphate binding loop can be seen interacting with the β and γ phosphates of ATP in the ATP-binding site proposed by Story and Steitz.<ref name=Story> Story, R. M.; Weber, I. T.; Steitz, T. A. The structure of the E. coli recA protein monomer and polymer. Nature (London) 1992, 355, 318-325. DOI: 10.1038/355318a0 </ref> The binding of various ligands to RecA has been shown to change the pitch, the “distance covered by each turn of the helix,” of the protein filament.<ref name=Ellouze> Ellouze, C.; Takahashi, M.; Wittung, P.; Mortensen, K.; Schnarr, M.; Nordén, B. Evidence for elongation of helical pitch of the helical pitch of the RecA filament upon ATP and ADP binding using small-angle neutron scattering. Eur. J. Biochem. 1995,233, 579-583. DOI: 10.1111/j.1432-1033.1995.579_2.x </ref> <ref name=Menetski> Menetski, J. P.; Kowalczykowski, S. C. Interaction of recA protein with single-stranded DNA: Quantitative aspects of binding affinity modulation by nucleotide cofactors. J. Mol. Biol. 1985, 181, 281-295. DOI: 10.1016/0022-2836(85)90092-0 </ref> RecA in the absence of any cofactor is in a “closed” conformation with a helical pitch of 7 nm (DNA binding to the RecA does not alter the pitch significantly). <scene name='41/413118/Reca_atp_complex/1'>RecA bound to ATP</scene> (ATP shown in Red/Organge) increases the pitch to 9 nm.<ref name=Ellouze> Ellouze, C.; Takahashi, M.; Wittung, P.; Mortensen, K.; Schnarr, M.; Nordén, B. Evidence for elongation of helical pitch of the helical pitch of the RecA filament upon ATP and ADP binding using small-angle neutron scattering. Eur. J. Biochem. 1995,233, 579-583. DOI: 10.1111/j.1432-1033.1995.579_2.x </ref> This RecA-ATP structure is marked by a higher affinity for DNA.<ref name=Roca> Roca, A. I.; Cox, M. M. RecA Protein: Structure, Function, and Role in Recombinational DNA Repair. Prog. Nucleic Acid Res. Mol. Biol. 1997, 56, 129-223. DOI: 10.1016/S0079-6603(08)61005-3 </ref> <ref name=Menetski> Menetski, J. P.; Kowalczykowski, S. C. Interaction of recA protein with single-stranded DNA: Quantitative aspects of binding affinity modulation by nucleotide cofactors. J. Mol. Biol. 1985, 181, 281-295. DOI: 10.1016/0022-2836(85)90092-0 </ref> However, the <scene name='41/413118/Reca_adp_complex/1'>binding of ADP to RecA</scene> (ADP in Red/Orange) only raises the pitch to 8.2 nm,<ref name=Ellouze> Ellouze, C.; Takahashi, M.; Wittung, P.; Mortensen, K.; Schnarr, M.; Nordén, B. Evidence for elongation of helical pitch of the helical pitch of the RecA filament upon ATP and ADP binding using small-angle neutron scattering. Eur. J. Biochem. 1995,233, 579-583. DOI: 10.1111/j.1432-1033.1995.579_2.x </ref> the conformation of which is known to have a lower affinity for DNA.<ref name=Roca> Roca, A. I.; Cox, M. M. RecA Protein: Structure, Function, and Role in Recombinational DNA Repair. Prog. Nucleic Acid Res. Mol. Biol. 1997, 56, 129-223. DOI: 10.1016/S0079-6603(08)61005-3 </ref> <ref name=Menetski> Menetski, J. P.; Kowalczykowski, S. C. Interaction of recA protein with single-stranded DNA: Quantitative aspects of binding affinity modulation by nucleotide cofactors. J. Mol. Biol. 1985, 181, 281-295. DOI: 10.1016/0022-2836(85)90092-0 </ref>

== RecA and Hofmeister Salts ==
High salt concentrations have also been shown to be able to elongate the RecA protein filament as well. Petukhov et al. demonstrated that a high concentration of NaCl increased the helical pitch from 7.8 to 8.6 nm.<ref name=Peukhov> Peukhov, M.; Lebedev, D.; Shalguev, V.; Islamov, A.; Kruklin, A.; Lanzov, V.; Isaev-Ivanov, V. Conformational Flexibility of RecA Protein Filament: Transitions between Compressed and Stretched States. Proteins: Struct.,Funct., Bioinf. 2006,65, 296-304. DOI: 10.1002/prot.21116 </ref> Thus, high salt concentrations appear to induce the active (stretched) form of RecA in the absence of DNA.<ref name=Peukhov> Peukhov, M.; Lebedev, D.; Shalguev, V.; Islamov, A.; Kruklin, A.; Lanzov, V.; Isaev-Ivanov, V. Conformational Flexibility of RecA Protein Filament: Transitions between Compressed and Stretched States. Proteins: Struct.,Funct., Bioinf. 2006,65, 296-304. DOI: 10.1002/prot.21116 </ref> Other studies have found that the free Magnesium ion binds to RecA (see <scene name='41/413118/Reca_adp_mg/3'>binding sites</scene>; Mg ion is colored lime green) and extends the filament more than 150% compared to the filament when DNA is bound.<ref name=Lusetti> Lusetti, S. L.; Shaw, J. J.; Cox, M. M. Magnesium Ion-dependent Activation of the RecA Protein
Involves the C Terminus. J. Biol. Chem. 2003, 278, 16381–16388. DOI: 10.1074/jbc.M212916200 </ref> Moreover, although normally RecA requires DNA to hydrolyze ATP, high salt concentrations are able to stimulate ATP hydrolysis in the absence of DNA.<ref name=Pugh> Pugh, B. F.; Cox, M. M. High Salt Activation of recA Protein ATPase in the Absence of DNA. J. Biol. Chem.1988, 263, 76-83. PMID: 2826451 </ref> Brenner and Zlotnick reported that the presence of monovalent salts changed the distribution of RecA aggregation states and that the more aggregated structures corresponded to higher protein concentration.<ref name=Brenner> Brenner, S. L.; Zlotnick, A. RecA Protein Self-assembly: Multiple Discrete Aggregation States. J. Mol. Biol. 1988, 204, 959-972. DOI: 10.1016/0022-2836(88)90055-1 </ref> Previous studies have shown that various Hofmeister salts affect the secondary structure, stability, and aggregation behavior of RecA differently.<ref name=Brenner> Brenner, S. L.; Zlotnick, A. RecA Protein Self-assembly: Multiple Discrete Aggregation States. J. Mol. Biol. 1988, 204, 959-972. DOI: 10.1016/0022-2836(88)90055-1 </ref> <ref name=Cannon> Cannon, W. R.; Talley, N. D.; Danzig, B. A.; Liu, X. L.; Martinez, J. S.; Shreve, A. P.; MacDonald, G. Ion specific influences on the stability and unfolding transitions of a naturally aggregating protein; RecA. Biophys. Chem. 2012, 163-164, 56-63. DOI: 10.1016/j.bpc.2012.02.005 </ref> Additionally, RecA has been demonstrated to follow the inverse-anionic Hofmeister series and the presence of some ions promotes nonspecific aggregation.<ref name=Cannon> Cannon, W. R.; Talley, N. D.; Danzig, B. A.; Liu, X. L.; Martinez, J. S.; Shreve, A. P.; MacDonald, G. Ion specific influences on the stability and unfolding transitions of a naturally aggregating protein; RecA. Biophys. Chem. 2012, 163-164, 56-63. DOI: 10.1016/j.bpc.2012.02.005 </ref>

==3D structures of recombinase A==
[[Recombinase A 3D structures]]
</StructureSection>
== References ==
<references/>

[[Category:Topic Page]]

3D structures of recombinase A

2026-10-04T09:04:24Z

Jaime Prilusky: Jaime Prilusky moved page 3D structures of recombinase A to Recombinase A 3D structures: using formal naming for 3D structures page

#REDIRECT [[Recombinase A 3D structures]]

Recombinase A 3D structures

2026-10-04T09:04:24Z

Jaime Prilusky: Jaime Prilusky moved page 3D structures of recombinase A to Recombinase A 3D structures: using formal naming for 3D structures page

== 3D Structures of Recombinase A ==

Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|

* RecA

**[[2oe2]], [[2ofo]], [[1ubc]] – ''Mycobacterium smegmatis''<br />
**[[2zr7]] – MsRecA form II’ – MsRecA<br />
**[[2zr0]] – MsRecA (mutant)<br />
**[[2zrb]] - MsRecA (mutant) form II’<br />
**[[2zrn]] - MsRecA (mutant) form IV<br />
**[[2zrc]], [[2zrh]] - MsRecA (mutant) form IV<br />
**[[1n03]], [[2reb]], [[3cmv]], [[4twz]] – EcRecA - ''Escherichia coli''<br />
**[[2rec]] – EcRecA - EM<br />
**[[1aa3]] – EcRecA C-terminal - NMR<br />
**[[1u94]] – EcRecA form II<br />
**[[1u98]] - EcRecA form III<br />
**[[1u99]] - EcRecA form IV<br />
**[[1g19]], [[4oqf]], [[4po1]], [[4po8]], [[4po9]], [[4poa]], [[4ppf]], [[4ppg]], [[4ppn]], [[4ppq]], [[4pqf]], [[4pqr]], [[4pqy]], [[4pr0]], [[4psa]], [[4psk]], [[4psv]], [[4ptl]] – MtRecA - ''Mycobacterium tuberculosis''<br />
**[[3ifj]], [[3igd]] – MtRecA (mutant)<br />
**[[3hr8]] – RecA – ''Thermotoga maritima''<br />
**[[5jrj]] – RecA – ''Herbaspirillum seropedicae''<br />

* RecA+nucleotides

**[[2zr9]] - MsRecA (mutant) form IV+dATP<br />
**[[2zra]] - MsRecA (mutant)+ATPgS<br />
**[[2zrg]], [[2zrl]], [[2zrp]] - MsRecA (mutant) form II’+dATP<br />
**[[2zrd]] - MsRecA (mutant) form IV+ADP<br />
**[[2zre]], [[2zrj]] - MsRecA (mutant) form IV+ATPgS<br />
**[[2zrf]], [[2zrk]], [[2zrm]] - MsRecA (mutant) form IV+dATP<br />
**[[2zri]], [[2zro]] - MsRecA (mutant) form IV+ADP<br />
**[[2odn]], [[2g88]], [[1ubg]] – MsRecA+dATP<br />
**[[2odw]], [[1ubf]] - MsRecA+ATPgS<br />
**[[2oep]], [[1ube]] - MsRecA+ADP<br />
**[[2oes]] - MsRecA+SSB<br />
**[[3cmt]], [[3cmu]], [[3cmw]], [[3cmx]] – EcRecA+SSDNA/DSDNA<br />
**[[1xms]] - EcRecA+Mn+AMP-PNP<br />
**[[1xmv]] - EcRecA+Mg+ADP<br />
**[[1rea]] - EcRecA+ADP<br />
**[[7jy6]], [[7jy7]], [[7jy8]], [[7jy9]] - EcRecA+ DNA + ATPgS – Cryo EM<br />
**[[1xp8]] – RecA+ATPgS – ''Deinococcus radiodurans''<br />
**[[1mo3]] – MtRecA+ADP<br />
**[[1mo4]] - MtRecA+ATPgS<br />
**[[1mo5]] - MtRecA+ATPgS+Mg<br />
**[[1mo6]] - MtRecA+dADP+Mg<br />
**[[1g18]] - MtRecA+ADP+AlF4<br />
**[[5j4j]] - RecA + ADP + ATP - ''Herbaspirillum seropedicae''<br />
**[[9uoo]] – RecA+ATPgS – ''Klebsiella pneumoniae''<br />

*RecA other complexes

**[[8gms]] – EcRecA + LexA – Cryo EM<br />
**[[8gmu]] – EcRecA + lambda repressor + DNA + ATPgS – Cryo EM<br />
**[[8gmt]] – EcRecA + DNA polymerase V subunit umud + DNA + ATPgS – Cryo EM<br />
**[[7ywa]] – EcRecA + DinI + DNA + ATPgS – Cryo EM<br />
**[[8amd]], [[8amf]] - RecA+ DNA + ATPgS – ''Streptococcus pneumoniae'' - Cryo EM<br />
**[[8s70]] – PaRecA + DNA – ''Pseudomonas aeruginosa'' – Cryo EM<br />
**[[8s7g]] – PaRecA + LexA + DNA – Cryo EM<br />

[[Category:Topic Page]]

Proteopedia:Development

2026-10-03T20:11:32Z

Jaime Prilusky:

See also:
* [[Proteopedia:Wishlist]]
* [[Proteopedia:Problems]]

==pending issues for Alcalá, November 2026==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]]''

(In the new server installation)

* SAT:
** color palette: restyling, colors ordered by HSL
** manage several isosurfaces in one model: a selector, color them individually, hide/display toggle
** add a choice of standard color palettes for surfaces (mostly gradients)
** add tooltips to describe surface coloring and possibility to have it added to the caption, as it was done for structure palettes

* New method for smooth transitions between scenes: fade-out, fade-in

* StructureSection:
** Links to Proteopedia pages may render wrong when some are inside StructureSection and some are outside
** Pages with more than one StructureSection have content misplaced

* Use PNGJ rather than state for saving the scenes

* Improve model pop-up window (JSmolPopup.htm and js)
** fix behaviour of resize buttons (in parent or popup)
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** descriptive window title, copying original caption
** adapt to parent page with more that one JSmol panels - make utility buttons specific for each applet

* Tutorial pages:
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** fix Ramachandran_Plot_Inspection

* Print3D
** check validity of output when 'scene' is selected as rendering style - dimensions, thicknesses
*** available print styles are restricted for large structures; when 'scene' is chosen, apparently restriction is not applied

* Adapt to handle new 12-character PDB_xxxxxxxx codes.

==Rehovot, September 2026==
''[[User:Jaime_Prilusky|JP]]''
* make more evident greenlinks by adding a yellow background
* add 'greenlink style' to Jmol buttons, since also interact with Jmol applet
* show PDB ID and 12-character extended PDB ID on seeded pages
* rebuild SAT to save and load scenes in PNGJ format
* rebuild mechanism to render different featured pages on each load of MainPage

==Online & at home, August-September 2024==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]]''
* An update of initialview script for seeded pages: combination into a single file, modularisation, fix for rendering of multimodel files.
* Introduced conditionalLoad function for deciding to skip simplified view, based on molecular weight of the biological unit with all models.
* New functions.spt combines many utility functions (including conditionalLoad)

* New look for toggle buttons (spin, quality, labels), popup button, load full button, resize buttons.
* Multimodel files: new toggle buttons: first/all models, animation on/off.

See [[Development/2024-09|details]].

==Rehovot, March 2023==
(12-20 March) ''[[User:Angel_Herraez|AH]], [[User:Jaime_Prilusky|JP]]'' and [[User:Joel_L._Sussman|JS]]:

=== Sequence Tool ===
This widget reads the information in any pdb- or mmcif-formatted file included in a Proteopedia page and parses its content to display the protein sequence (for all chains) alongside the JSmol 3D-view panel.
The sequence includes information combined from both the COORD and SEQRES records in the PDB file, hence including physical gaps, numbering gaps, sequence microheterogeneity and inserted residues.

The visitor of the page may interactively explore the structure and the sequence:
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This tool is included in all pages automatically generated in Proteopedia for any new structure
deposited in the Protein Data Bank (seeded pages) and may be included at will in user-generated
pages. Documentation is at [[Seqtool]]

=== Colouring schemes for AI-predicted structures ===
Procedures were developed to apply several colouring schemes in the 3D structure view that reflect the reliability or uncertainty in the coordinates of each residue in predicted 3D protein structures coming form several platforms and databases, namely:
* [https://robetta.bakerlab.org RoseTTAFold], with RMSD data for each atom or residue.
* [https://alphafold.ebi.ac.uk AlphaFold], with pLDDT score for each atom or residue.
* [https://esmatlas.com/about#fold ESMFold], with pLDDT score for each atom or residue.
The functionality for applying these colour schemes was added through buttons in the SAT, and it is offered automatically depending on which data source provides the uploaded structure files.

The colour reference (legend) is automatically included below the caption area under the 3D view, for any new scene that was created using the colouring option.
[[Image:AI-predicted coloring schemes.png]]

===Prediction of structure===
A new area inside 'load molecule' section of SAT allows to enter a raw or Fasta-formatted protein
sequence, sends it to the ESMfold server and retrieves the resulting predicted structure into
Proteopedia. The structure is also loaded on SAT, ready for preparing a scene.

==Alcalá, Spain, March 2021==
[[User:Angel_Herraez|AH]] modified Html5mediator.php to allow embedding videos from [https://vimeo.com Vimeo]

==Rehovot December 2020==
[[User:Jaime_Prilusky|JP]]:
* Enabled Proteopedia to manage scenes with multiple isosurfaces.
* Modified SAT to allow adding multiple isosurfaces to a scene and to edit scenes with multiple isosurfaces.
* Incorporated CSS class bg- and text- to allow coloring of captions and text.

==Rehovot October 2020==
[[User:Jaime_Prilusky|JP]]: Modified SAT's scene searching approach to ease reuse scenes from other pages. SAT now scan the page being edited for ''name='##/wgArticleId/'' and build the scenes dropdown on [load scene] tab with all the scenes from all the wgArticleIds found.

==Rehovot, January 2019==
[[User:Jaime_Prilusky|JP]] and [[User:Joel_L._Sussman|JS]]: Morphing on Proteopedia at [[Special:Morph]]. Provide two structures (either PDB ids, upload files or a combination or both) and optional chain selection and click Morph. Morphing takes place between a few minutes, thanks to PyMOL and SCHRODINGER, and you’ll be able to directly upload the resulting morph to Proteopedia for SAT scene development, or download a PDB or .pse file.

==Rehovot, October 2018==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working together during AH's visit to Weizmann Institute, 12 to 19 October 2018.''
* JSmol was upgraded to version 14.29.16
* A conflict was solved between display of PDB file information (e.g. resolution, nr.of NMR models) and display of caption.
* SAT: the chosen options for a scene (description, caption, spin status, scene transitions...) are now stored together with the scene and hence they are reused as defaults when the scene is edited.
* More work on connecting the Sequence display with the Structure.
* Use WebGL for rendering, enabled per user (new toggle in the Preferences page). Note that not all features in JSmol are implemented in WebGL, so customised scenes may lack features; you can check a list of supported and unsupported features [http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/WebGL#Support_for_JmolScript_features here]. This is experimental and still needs some work (e.g. Simplified and Full model do not make sense in WebGL; also we need to verify proper display of ligands)
* Work on a new design for the home page.

== Rehovot, August 2018 ==
[[User:Jaime_Prilusky|JP]] JSmol applet displays "I'm ready. Click on a green link" when there's no defined structure or scene to render. Before, it remained with the "Loading, please wait ..." statement forever, since there was nothing to load.

== Alcalá, Spain, March 2018 ==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working side by side during JP's visit to Alcalá, 19 to 22 March 2018.''

* Files can now be dragged from local disk and dropped onto the SAT. A copy of the file will be automatically uploaded and stored in Proteopedia and will be subsequently used by the scenes that are created from that SAT.
* The SAT, under ''Load molecule'', now has an option to load the ''Biological Assembly'' rather than the ''Asymmetric Unit'' (which was previously the only choice and will still be the default).
* Additional work on the special interface for display of knowledge about mutations of some deeply studied proteins. Different renderings, added onto the protein's 3D structure, were implemented for each kind of feature that results from the mutation.

== Amherst, MA, USA, January 2018 ==
Proteopedia 10th Anniversary Conference
* An option to use the latest version of JSmol while viewing any Proteopedia page has been added to the user's [[Special:Preferences|personal preferences]] section: click on the ‘Misc’ tab and check the option to ‘use the latest JSmol version’; then, save your preferences.
** JSmol files will be retrieved from <nowiki>https://chemapps.stolaf.edu/jmol/jsmol</nowiki>
* Advanced users will found now in Proteopedia’s Scene Authoring Tool (SAT), under the JSmol panel, a button to quickly open JSmol Script Console and a text input field to enter scripting commands and Execute them. This allows to easily execute additional scripting JSmol commands besides those currently implemented as buttons and pulldowns.

== Essen, Germany, June 2017 ==
[[User:Jaime_Prilusky|JP]] Added option to load= attribute to indicate if to load Asymmetric Unit or Biological Assembly for a PDB structure, by adding _au or _ba to the PDB id ( i.e load=2ace_au load=2ace_ba ). Default behaviour, when only the PDB id is provided, remains the same: loads Biological Assembly if available, otherwise the Asymmetric Unit.

== Rehovot, Israel, June 2017 ==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working side by side during AH's visit to Weizmann, 30 May to 13 June 2017, with constant feedback from [[User:Joel_L._Sussman|JS]]''

During this period we addressed an update in the back-end features of the Proteopedia platform. The major aim was to improve the user experience in the platform, as well as adding some new features.

Several features were implemented in Proteopedia and were immediately made available online for the users. Changes were applied to the design of Proteopedia pages, particularly aiming to speed up the loading and increase responsiveness of pages for the user. The drop of web browser support for Java applets along the previous years led us (2014) to implement the use of the JSmol viewer for structures, in place of the former Jmol viewer. However, that brought the inconvenience of a slower response. In these new developments (2017), we made some changes that reduce the delay associated to including JSmol in the pages.

* The JSmol object is now written to the page not during, but after page loading has completed.
** Even though page loading speed is not perceivable enhanced, such delayed insertion has allowed to implement several other functionalities added to Proteopedia pages.
* A rotating image (animated gif) for the model or scene is displayed initially in place of the JSmol object (when such gif file is already available). Therefore, the initial delay on page loading is now suppressed and it will take place only when the user requests JSmol to load. This allows much quicker loading of the page.
** Proteopedia Main Page is now using those animated images with its front models (selected randomly out of a short list). This results in a much more quickly responding page.
** A new button [''Display Interactive Model''] is shown below the image, for the user to decide showing the JSmol model instead of the initial replacement image.
** The image is replaced with the JSmol model also whenever the user clicks on a green link.
** An automated procedure allows to generate and save the animated GIFs for Proteopedia seeded pages, as well as for user-authored pages. This procedure is to be used programmatically for the full collection, or manually just by privileged users.
* The JSmol panel in all pages is now resizable. This will allow adjustment by the users, according to their device screen size, the diverse needs and the intended use, e.g. projection in the classroom.
** Two new buttons were added in the tool area below the JSmol panel, to increase and decrease the size in discrete steps (20%, within a range from 200 to 800 px).
** The [''popup''] button is still available as an independent option.
* The popup window now has a new extra button, [''update''], that allows to refresh the state of model, retrieving it again from the calling page. This avoids the need to call again the popup window and load again the JSmol object (so it yields a quicker experience). It also allows, for example, to work in the page on the main monitor while displaying the enlarged model (popup) in a second monitor or projector.
* All the above-mentioned new options have also been added as part of the [[http://proteopedia.org/w/User:Jaime_Prilusky/JSmolExtension|JSmol Extension for MediaWiki]], for use in other websites.
* When entering page ''Edit mode'', JSmol for the ''Scene Authoring Tool'' (SAT) is not inserted until the user opens the SAT by clicking on the [show] button. This results in a much more quickly responding page, allowing for quick editing of the page text if changing scenes was not intended. The delay that used to be on loading the page has now been shifted to when the user decides to open the SAT (and only the first time).
* Whenever a model is loaded (seeded pages at least), information is filled into the page content, under the JSmol page:
** The PDB id (read from the server).
** Number of models if NMR. This is read from the server or from within JSmol.
** Resolution if applicable. (Implementation is pending)
** Type of model: ''biological assembly'' or ''asymmetric unit''. This is read from the Proteopedia server.
* When creating a scene, the user may specify a caption; this will be saved together with the scene and will be displayed in the page when any user clicks on the green link to loads that scene into the JSmol panel. This caption is inserted in the area below the model.
** The caption will be updated whenever a new scene is loaded (as long as the scene was prepared and saved including a caption).
* For seeded pages, any user has now a choice to display the model of either ''biological assembly'' or ''asymmetric unit'', as long as the files are available in the server for that particular protein. If only one is available, only the relevant option is presented in the interface.
* When a page is written in a language other than English and its title has been set as recommended (that is, ''Title of page (language)''), the JSmol interface (context menu) is now displayed in the language matching the page. This possibility is limited to those languages for which there is a Jmol localisation; otherwise, the default for JSmol is the system language, otherwise US English. Examples: [[1eve_%28Spanish%29|Spanish]], [[1eve_%28French%29|French]], [[1eve_%28German%29|German]], [[1eve_%28Italian%29|Italian]], [[1eve_%28Czech%29|Czech]], [[1eve_%28Russian%29|Russian]], [[1eve_%28Turkish%29|Turkish]], [[1eve_%28Chinese%29|Chinese]].

Additionally, we started development of a wholly new approach: to develop a visual interface that incorporates knowledge about mutations of some deeply studied proteins, their effect on structure and stability of the molecule, so as to gain insights into what structural alterations are relevant to pathogenicity.

* A special page will hold the sequence and mutation data. This page may be edited as usual, by authorised users.
* The display page, also editable,
** Has a regular content area, editable by users.
** Reads the data from the matching data page (access limited).
** Includes a scrollable panel showing the sequence of the protein, with all mutations listed.
** Includes the JSmol model.
** Clicking on the mutations displays them in the 3D model, focusing on the affected residue, with highlights on the neighbouring residues and display of clashes.
** The display in JSmol may be animated between wild type and mutated residue.

== Alcalá, Spain, October 2016 ==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working side by side during JP's visit to Alcalá, 10 to 13 October 2016.''

=== Template for ConSurf ===
A mediawiki template, [[Template:ConSurf|{ {ConSurf} }]], was written that inserts the standard ConSurf subsection, including description, links and the checkbox to apply the evolutionary conservation colouring, applied to the protein specified by the user editing any page.

Pending:
* Write documentation or help, possibly combining it with [[Help:How_to_Insert_a_ConSurf_Result_Into_a_Proteopedia_Green_Link|existing help]]

=== Update of style applied by the "high quality" button ===

This button is located under every model (JSmol panel).

It formerly toggled the <code>antialiasDisplay</code> state.

It is now changed to also toggle the use of <code>cartoonFancy</code>.

Note: the high quality mode is abandoned during rotation, but gives a nicer look when stopped, e.g. for copying an image. It may be retained during rotation if the default in Proteopedia, <code>platformSpeed 5</code>, is changed to at least 6 e.g. using the <code>pspeed</code> option in the applet tag (not advisable in general for responsiveness in mobile platforms).

=== Direct insertion of the scene link from SAT into the body text ===

When a scene is saved within the SAT, the former method required the author to copy some resulting code with the scene green link from a textbox in the SAT to the editable section (wikitext) of the page content.

The improvement implemented adds the scene code automatically at the current cursor position within the editable content.

Pending:
* Adequate help needs to be written and inserted, particularly to instruct the user to have the cursor in the right place before saving the scene.
* Maybe remove or hide the textbox in the SAT, to avoid duplicity or confusion.

=== Generation of animated image with rotating model ===

A link, “Export Animated Image” has been added in the area below the JSmol panel. This allows to obtain an animated GIF of the current scene, useful for display in presentations or web pages independent from Proteopedia.

The animation is produced server-side (using Jmol.jar and ImageMagick).

Technical: the use of the capture command in Jmol proved to be impossible without a graphic display; therefore, we had to resort to using a loop with incremental rotation and single image export at each step, then combine them all into a single animated gif.
A full 360° spin is implemented, with some user choices like axis of rotation, overall duration of one full turn in the animation, dimensions and smoothness of the animation.

Pending:
* Add better help / explanation of the process, and how to download the resulting image. #DONE
* Implement also the “rocking” motion as an alternative animated display. #DONE

=== Compaction of JSmol pop-up menu ===

The menu has been increasing in length and complexity along Jmol versions. Some actions were taken so that if fits better in available window space. Only css was used, which overrides the default css rules included in the JSmol library.
* Reduced line height for each submenu entry (not only first level entries but also all submenus)
* The languages submenu is now scrollable within a limited height.
Pending:
* Investigate: the popup menu in the SAT seems to be able to open upwards when there is no space at the bottom of window. Achieving this would be desirable for JSmol in general. It may be caused by action of some other jQuery UI code, in effect only in the SAT but absent in JSmol’s copy of UI.

=== Rendering of nucleotide ligands ===

In the default initial rendering, ligands are displayed as spacefill cpk. However, JSmol fails to identify single nucleotides as ligands (they are evaluated as single-residue nucleic acids and so rendered as cartoon, i.e. invisible).

Code was added to <code>initialview02v3.spt</code> so that single nucleotides are rendered like ligands (e.g. GDP, GTP often bound to G-proteins, or ATP in kinases)

=== Access to SAT not available ===

The banner and link to open the SAT is not displayed while the page is being edited and the Preview has been requested. As a consequence, if the user under<code> My preferences > Editing </code>checks the<code> Show preview on first edit </code>option, he will never see the SAT.

A hint for this was added to [[Help:Contents#Creating_Molecular_Scenes]]

=== Issues detected that need further work or investigation ===

==== Using assembly CIF ====
Limitations associated to using mmCIF assemblies as the source of models.
* <code>biopolymers</code> are not detected by Jmol (as chosen from the pop-up menu), or not available due to asemblies?
* Need to check the status of retrieval of biological unit vs. asymmetric unit. #DONE
* Ned to check different behaviour in applet tag than in SAT, e.g. the display of tetramer vs. dimer – likely related to the use of <code>getlateststructure</code> or <code>getfrozenstructure</code> and the recent switch to using assemblies
* Some ligands are not listed under Hetero in the popup menu. Example: [UIR] in [[Trypsin]] or [[1y3v]]

==== Transitions between scenes ====
SAT offers some options for transitions (skip zoom-out, skip transition), the behaviour of which needs to be re-checked. They might be not working, or rather be incompatible with the option of reloading the model for each new scene.

==== Update caption below structure for each scene ====
Below the JSmol model a caption is displayed, with text specified in the applet tag. When a different scene is loaded, this caption should get updated.

(Remains to be implemented) #DONE

==== Choice of templates for a new page ====
When a new page is started, it is created with a template. The possibility of offering a gallery of templates or layouts was suggested.

This was not addressed for lack of specific ideas. Not clear if it would be useful. #DISREGARDED

==== Category:Pyrho ====
[[:Category:Pyrho]] which is very frequent, inserts a bad link to Wikipedia (non existing page).

==== Localisation ====
* When a page is written in a non-English language, the language of the JSmol interface could be changed to match. [[Aricept_Complexed_with_Acetylcholinesterase_%28French%29|Example in French]] #DONE

Proteopedia:Development

2026-10-03T20:10:21Z

Jaime Prilusky:

See also:
* [[Proteopedia:Wishlist]]
* [[Proteopedia:Problems]]

==pending issues for Alcalá, November 2026==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]]''

(In the new server installation)

* SAT:
** color palette: restyling, colors ordered by HSL
** manage several isosurfaces in one model: a selector, color them individually, hide/display toggle
** add a choice of standard color palettes for surfaces (mostly gradients)
** add tooltips to describe surface coloring and possibility to have it added to the caption, as it was done for structure palettes

* New method for smooth transitions between scenes: fade-out, fade-in

* StructureSection:
** Links to Proteopedia pages may render wrong when some are inside StructureSection and some are outside
** Pages with more than one StructureSection have content misplaced

* Use PNGJ rather than state for saving the scenes

* Improve model pop-up window (JSmolPopup.htm and js)
** fix behaviour of resize buttons (in parent or popup)
** better refresh (avoid errors)
** descriptive window title, copying original caption
** adapt to parent page with more that one JSmol panels - make utility buttons specific for each applet

* Tutorial pages:
** fix Ramachandran_principle_and_phi_psi_angles
** fix Ramachandran_Plot_Inspection

* Print3D
** check validity of output when 'scene' is selected as rendering style - dimensions, thicknesses
*** available print styles are restricted for large structures; when 'scene' is chosen, apparently restriction is not applied

* Adapt to handle new 12-character PDB_xxxxxxxx codes.

==Rehovot, September 2026==
''[[User:Jaime_Prilusky|JP]]''
* make more evident greenlinks by adding a yellow background
* add 'greenlink style' to Jmol buttons, since also interact with Jmol applet
* show PDB ID and 12-character extended PDB ID on seeded pages
* rebuild SAT to save and load scenes in PNGJ format
* rebuild mechanism to render different featured pages on each loading of MainPage

==Online & at home, August-September 2024==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]]''
* An update of initialview script for seeded pages: combination into a single file, modularisation, fix for rendering of multimodel files.
* Introduced conditionalLoad function for deciding to skip simplified view, based on molecular weight of the biological unit with all models.
* New functions.spt combines many utility functions (including conditionalLoad)

* New look for toggle buttons (spin, quality, labels), popup button, load full button, resize buttons.
* Multimodel files: new toggle buttons: first/all models, animation on/off.

See [[Development/2024-09|details]].

==Rehovot, March 2023==
(12-20 March) ''[[User:Angel_Herraez|AH]], [[User:Jaime_Prilusky|JP]]'' and [[User:Joel_L._Sussman|JS]]:

=== Sequence Tool ===
This widget reads the information in any pdb- or mmcif-formatted file included in a Proteopedia page and parses its content to display the protein sequence (for all chains) alongside the JSmol 3D-view panel.
The sequence includes information combined from both the COORD and SEQRES records in the PDB file, hence including physical gaps, numbering gaps, sequence microheterogeneity and inserted residues.

The visitor of the page may interactively explore the structure and the sequence:
* A click on a letter in the sequence listing will display the full information of that residue and will highlight it in the 3D structure view.
* A click on any atom in the 3D view will highlight the matching residue in the sequence listing.
* A search box accepts a residue number, or a residue letter, or a partial sequence; matches will be displayed on both the sequence and the structure.

This tool is included in all pages automatically generated in Proteopedia for any new structure
deposited in the Protein Data Bank (seeded pages) and may be included at will in user-generated
pages. Documentation is at [[Seqtool]]

=== Colouring schemes for AI-predicted structures ===
Procedures were developed to apply several colouring schemes in the 3D structure view that reflect the reliability or uncertainty in the coordinates of each residue in predicted 3D protein structures coming form several platforms and databases, namely:
* [https://robetta.bakerlab.org RoseTTAFold], with RMSD data for each atom or residue.
* [https://alphafold.ebi.ac.uk AlphaFold], with pLDDT score for each atom or residue.
* [https://esmatlas.com/about#fold ESMFold], with pLDDT score for each atom or residue.
The functionality for applying these colour schemes was added through buttons in the SAT, and it is offered automatically depending on which data source provides the uploaded structure files.

The colour reference (legend) is automatically included below the caption area under the 3D view, for any new scene that was created using the colouring option.
[[Image:AI-predicted coloring schemes.png]]

===Prediction of structure===
A new area inside 'load molecule' section of SAT allows to enter a raw or Fasta-formatted protein
sequence, sends it to the ESMfold server and retrieves the resulting predicted structure into
Proteopedia. The structure is also loaded on SAT, ready for preparing a scene.

==Alcalá, Spain, March 2021==
[[User:Angel_Herraez|AH]] modified Html5mediator.php to allow embedding videos from [https://vimeo.com Vimeo]

==Rehovot December 2020==
[[User:Jaime_Prilusky|JP]]:
* Enabled Proteopedia to manage scenes with multiple isosurfaces.
* Modified SAT to allow adding multiple isosurfaces to a scene and to edit scenes with multiple isosurfaces.
* Incorporated CSS class bg- and text- to allow coloring of captions and text.

==Rehovot October 2020==
[[User:Jaime_Prilusky|JP]]: Modified SAT's scene searching approach to ease reuse scenes from other pages. SAT now scan the page being edited for ''name='##/wgArticleId/'' and build the scenes dropdown on [load scene] tab with all the scenes from all the wgArticleIds found.

==Rehovot, January 2019==
[[User:Jaime_Prilusky|JP]] and [[User:Joel_L._Sussman|JS]]: Morphing on Proteopedia at [[Special:Morph]]. Provide two structures (either PDB ids, upload files or a combination or both) and optional chain selection and click Morph. Morphing takes place between a few minutes, thanks to PyMOL and SCHRODINGER, and you’ll be able to directly upload the resulting morph to Proteopedia for SAT scene development, or download a PDB or .pse file.

==Rehovot, October 2018==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working together during AH's visit to Weizmann Institute, 12 to 19 October 2018.''
* JSmol was upgraded to version 14.29.16
* A conflict was solved between display of PDB file information (e.g. resolution, nr.of NMR models) and display of caption.
* SAT: the chosen options for a scene (description, caption, spin status, scene transitions...) are now stored together with the scene and hence they are reused as defaults when the scene is edited.
* More work on connecting the Sequence display with the Structure.
* Use WebGL for rendering, enabled per user (new toggle in the Preferences page). Note that not all features in JSmol are implemented in WebGL, so customised scenes may lack features; you can check a list of supported and unsupported features [http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/WebGL#Support_for_JmolScript_features here]. This is experimental and still needs some work (e.g. Simplified and Full model do not make sense in WebGL; also we need to verify proper display of ligands)
* Work on a new design for the home page.

== Rehovot, August 2018 ==
[[User:Jaime_Prilusky|JP]] JSmol applet displays "I'm ready. Click on a green link" when there's no defined structure or scene to render. Before, it remained with the "Loading, please wait ..." statement forever, since there was nothing to load.

== Alcalá, Spain, March 2018 ==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working side by side during JP's visit to Alcalá, 19 to 22 March 2018.''

* Files can now be dragged from local disk and dropped onto the SAT. A copy of the file will be automatically uploaded and stored in Proteopedia and will be subsequently used by the scenes that are created from that SAT.
* The SAT, under ''Load molecule'', now has an option to load the ''Biological Assembly'' rather than the ''Asymmetric Unit'' (which was previously the only choice and will still be the default).
* Additional work on the special interface for display of knowledge about mutations of some deeply studied proteins. Different renderings, added onto the protein's 3D structure, were implemented for each kind of feature that results from the mutation.

== Amherst, MA, USA, January 2018 ==
Proteopedia 10th Anniversary Conference
* An option to use the latest version of JSmol while viewing any Proteopedia page has been added to the user's [[Special:Preferences|personal preferences]] section: click on the ‘Misc’ tab and check the option to ‘use the latest JSmol version’; then, save your preferences.
** JSmol files will be retrieved from <nowiki>https://chemapps.stolaf.edu/jmol/jsmol</nowiki>
* Advanced users will found now in Proteopedia’s Scene Authoring Tool (SAT), under the JSmol panel, a button to quickly open JSmol Script Console and a text input field to enter scripting commands and Execute them. This allows to easily execute additional scripting JSmol commands besides those currently implemented as buttons and pulldowns.

== Essen, Germany, June 2017 ==
[[User:Jaime_Prilusky|JP]] Added option to load= attribute to indicate if to load Asymmetric Unit or Biological Assembly for a PDB structure, by adding _au or _ba to the PDB id ( i.e load=2ace_au load=2ace_ba ). Default behaviour, when only the PDB id is provided, remains the same: loads Biological Assembly if available, otherwise the Asymmetric Unit.

== Rehovot, Israel, June 2017 ==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working side by side during AH's visit to Weizmann, 30 May to 13 June 2017, with constant feedback from [[User:Joel_L._Sussman|JS]]''

During this period we addressed an update in the back-end features of the Proteopedia platform. The major aim was to improve the user experience in the platform, as well as adding some new features.

Several features were implemented in Proteopedia and were immediately made available online for the users. Changes were applied to the design of Proteopedia pages, particularly aiming to speed up the loading and increase responsiveness of pages for the user. The drop of web browser support for Java applets along the previous years led us (2014) to implement the use of the JSmol viewer for structures, in place of the former Jmol viewer. However, that brought the inconvenience of a slower response. In these new developments (2017), we made some changes that reduce the delay associated to including JSmol in the pages.

* The JSmol object is now written to the page not during, but after page loading has completed.
** Even though page loading speed is not perceivable enhanced, such delayed insertion has allowed to implement several other functionalities added to Proteopedia pages.
* A rotating image (animated gif) for the model or scene is displayed initially in place of the JSmol object (when such gif file is already available). Therefore, the initial delay on page loading is now suppressed and it will take place only when the user requests JSmol to load. This allows much quicker loading of the page.
** Proteopedia Main Page is now using those animated images with its front models (selected randomly out of a short list). This results in a much more quickly responding page.
** A new button [''Display Interactive Model''] is shown below the image, for the user to decide showing the JSmol model instead of the initial replacement image.
** The image is replaced with the JSmol model also whenever the user clicks on a green link.
** An automated procedure allows to generate and save the animated GIFs for Proteopedia seeded pages, as well as for user-authored pages. This procedure is to be used programmatically for the full collection, or manually just by privileged users.
* The JSmol panel in all pages is now resizable. This will allow adjustment by the users, according to their device screen size, the diverse needs and the intended use, e.g. projection in the classroom.
** Two new buttons were added in the tool area below the JSmol panel, to increase and decrease the size in discrete steps (20%, within a range from 200 to 800 px).
** The [''popup''] button is still available as an independent option.
* The popup window now has a new extra button, [''update''], that allows to refresh the state of model, retrieving it again from the calling page. This avoids the need to call again the popup window and load again the JSmol object (so it yields a quicker experience). It also allows, for example, to work in the page on the main monitor while displaying the enlarged model (popup) in a second monitor or projector.
* All the above-mentioned new options have also been added as part of the [[http://proteopedia.org/w/User:Jaime_Prilusky/JSmolExtension|JSmol Extension for MediaWiki]], for use in other websites.
* When entering page ''Edit mode'', JSmol for the ''Scene Authoring Tool'' (SAT) is not inserted until the user opens the SAT by clicking on the [show] button. This results in a much more quickly responding page, allowing for quick editing of the page text if changing scenes was not intended. The delay that used to be on loading the page has now been shifted to when the user decides to open the SAT (and only the first time).
* Whenever a model is loaded (seeded pages at least), information is filled into the page content, under the JSmol page:
** The PDB id (read from the server).
** Number of models if NMR. This is read from the server or from within JSmol.
** Resolution if applicable. (Implementation is pending)
** Type of model: ''biological assembly'' or ''asymmetric unit''. This is read from the Proteopedia server.
* When creating a scene, the user may specify a caption; this will be saved together with the scene and will be displayed in the page when any user clicks on the green link to loads that scene into the JSmol panel. This caption is inserted in the area below the model.
** The caption will be updated whenever a new scene is loaded (as long as the scene was prepared and saved including a caption).
* For seeded pages, any user has now a choice to display the model of either ''biological assembly'' or ''asymmetric unit'', as long as the files are available in the server for that particular protein. If only one is available, only the relevant option is presented in the interface.
* When a page is written in a language other than English and its title has been set as recommended (that is, ''Title of page (language)''), the JSmol interface (context menu) is now displayed in the language matching the page. This possibility is limited to those languages for which there is a Jmol localisation; otherwise, the default for JSmol is the system language, otherwise US English. Examples: [[1eve_%28Spanish%29|Spanish]], [[1eve_%28French%29|French]], [[1eve_%28German%29|German]], [[1eve_%28Italian%29|Italian]], [[1eve_%28Czech%29|Czech]], [[1eve_%28Russian%29|Russian]], [[1eve_%28Turkish%29|Turkish]], [[1eve_%28Chinese%29|Chinese]].

Additionally, we started development of a wholly new approach: to develop a visual interface that incorporates knowledge about mutations of some deeply studied proteins, their effect on structure and stability of the molecule, so as to gain insights into what structural alterations are relevant to pathogenicity.

* A special page will hold the sequence and mutation data. This page may be edited as usual, by authorised users.
* The display page, also editable,
** Has a regular content area, editable by users.
** Reads the data from the matching data page (access limited).
** Includes a scrollable panel showing the sequence of the protein, with all mutations listed.
** Includes the JSmol model.
** Clicking on the mutations displays them in the 3D model, focusing on the affected residue, with highlights on the neighbouring residues and display of clashes.
** The display in JSmol may be animated between wild type and mutated residue.

== Alcalá, Spain, October 2016 ==
''[[User:Angel_Herraez|AH]] and [[User:Jaime_Prilusky|JP]] working side by side during JP's visit to Alcalá, 10 to 13 October 2016.''

=== Template for ConSurf ===
A mediawiki template, [[Template:ConSurf|{ {ConSurf} }]], was written that inserts the standard ConSurf subsection, including description, links and the checkbox to apply the evolutionary conservation colouring, applied to the protein specified by the user editing any page.

Pending:
* Write documentation or help, possibly combining it with [[Help:How_to_Insert_a_ConSurf_Result_Into_a_Proteopedia_Green_Link|existing help]]

=== Update of style applied by the "high quality" button ===

This button is located under every model (JSmol panel).

It formerly toggled the <code>antialiasDisplay</code> state.

It is now changed to also toggle the use of <code>cartoonFancy</code>.

Note: the high quality mode is abandoned during rotation, but gives a nicer look when stopped, e.g. for copying an image. It may be retained during rotation if the default in Proteopedia, <code>platformSpeed 5</code>, is changed to at least 6 e.g. using the <code>pspeed</code> option in the applet tag (not advisable in general for responsiveness in mobile platforms).

=== Direct insertion of the scene link from SAT into the body text ===

When a scene is saved within the SAT, the former method required the author to copy some resulting code with the scene green link from a textbox in the SAT to the editable section (wikitext) of the page content.

The improvement implemented adds the scene code automatically at the current cursor position within the editable content.

Pending:
* Adequate help needs to be written and inserted, particularly to instruct the user to have the cursor in the right place before saving the scene.
* Maybe remove or hide the textbox in the SAT, to avoid duplicity or confusion.

=== Generation of animated image with rotating model ===

A link, “Export Animated Image” has been added in the area below the JSmol panel. This allows to obtain an animated GIF of the current scene, useful for display in presentations or web pages independent from Proteopedia.

The animation is produced server-side (using Jmol.jar and ImageMagick).

Technical: the use of the capture command in Jmol proved to be impossible without a graphic display; therefore, we had to resort to using a loop with incremental rotation and single image export at each step, then combine them all into a single animated gif.
A full 360° spin is implemented, with some user choices like axis of rotation, overall duration of one full turn in the animation, dimensions and smoothness of the animation.

Pending:
* Add better help / explanation of the process, and how to download the resulting image. #DONE
* Implement also the “rocking” motion as an alternative animated display. #DONE

=== Compaction of JSmol pop-up menu ===

The menu has been increasing in length and complexity along Jmol versions. Some actions were taken so that if fits better in available window space. Only css was used, which overrides the default css rules included in the JSmol library.
* Reduced line height for each submenu entry (not only first level entries but also all submenus)
* The languages submenu is now scrollable within a limited height.
Pending:
* Investigate: the popup menu in the SAT seems to be able to open upwards when there is no space at the bottom of window. Achieving this would be desirable for JSmol in general. It may be caused by action of some other jQuery UI code, in effect only in the SAT but absent in JSmol’s copy of UI.

=== Rendering of nucleotide ligands ===

In the default initial rendering, ligands are displayed as spacefill cpk. However, JSmol fails to identify single nucleotides as ligands (they are evaluated as single-residue nucleic acids and so rendered as cartoon, i.e. invisible).

Code was added to <code>initialview02v3.spt</code> so that single nucleotides are rendered like ligands (e.g. GDP, GTP often bound to G-proteins, or ATP in kinases)

=== Access to SAT not available ===

The banner and link to open the SAT is not displayed while the page is being edited and the Preview has been requested. As a consequence, if the user under<code> My preferences > Editing </code>checks the<code> Show preview on first edit </code>option, he will never see the SAT.

A hint for this was added to [[Help:Contents#Creating_Molecular_Scenes]]

=== Issues detected that need further work or investigation ===

==== Using assembly CIF ====
Limitations associated to using mmCIF assemblies as the source of models.
* <code>biopolymers</code> are not detected by Jmol (as chosen from the pop-up menu), or not available due to asemblies?
* Need to check the status of retrieval of biological unit vs. asymmetric unit. #DONE
* Ned to check different behaviour in applet tag than in SAT, e.g. the display of tetramer vs. dimer – likely related to the use of <code>getlateststructure</code> or <code>getfrozenstructure</code> and the recent switch to using assemblies
* Some ligands are not listed under Hetero in the popup menu. Example: [UIR] in [[Trypsin]] or [[1y3v]]

==== Transitions between scenes ====
SAT offers some options for transitions (skip zoom-out, skip transition), the behaviour of which needs to be re-checked. They might be not working, or rather be incompatible with the option of reloading the model for each new scene.

==== Update caption below structure for each scene ====
Below the JSmol model a caption is displayed, with text specified in the applet tag. When a different scene is loaded, this caption should get updated.

(Remains to be implemented) #DONE

==== Choice of templates for a new page ====
When a new page is started, it is created with a template. The possibility of offering a gallery of templates or layouts was suggested.

This was not addressed for lack of specific ideas. Not clear if it would be useful. #DISREGARDED

==== Category:Pyrho ====
[[:Category:Pyrho]] which is very frequent, inserts a bad link to Wikipedia (non existing page).

==== Localisation ====
* When a page is written in a non-English language, the language of the JSmol interface could be changed to match. [[Aricept_Complexed_with_Acetylcholinesterase_%28French%29|Example in French]] #DONE

User:Jaime Prilusky/Test/Surfaces

2026-10-03T16:40:00Z

Jaime Prilusky:

==Your Heading Here (maybe something like 'Structure')==
<StructureSection load='' size='340' side='right' caption='' scene=''>

* <scene name='11/1109340/1crn/3'>1crn</scene> color cartoon+surface
* <scene name='11/1109340/1crn/4'>1crn</scene> color cartoon

* <scene name='11/1109340/3rec/1'>3rec</scene>

</StructureSection>
== References ==
<references/>

Proteopedia:I3DC

2026-10-03T10:47:21Z

Jaime Prilusky:

__NOEDITSECTION__
===Acta Cryst D ''Acta Crystallographica Section D''===
# [[Journal:Acta Cryst D:S0907444911047251|Flexibility of the flap in the active site of BACE1 as revealed by crystal structures and molecular dynamics simulations]], Yechun Xu, Minjun Li, Harry Greenblatt, Wuyan Chen, Aviv Paz, Orly Dym, Yoav Peleg, Tiantian Chen, Xu Shen, Jianhua He, Hualiang Jiang, Israel Silman & Joel L Sussman
# [[Journal:Acta Cryst D:S2059798318000050|A DNA structural alphabet provides new insight into DNA flexibility]], Bohdan Schneider, Paulina Bozikova, Iva Necasova, Petr Cech, Daniel Svozil and Jiri Cerny
# [[Journal:Acta Cryst D:S2059798318014900|Structure of the AmyC GH13 alpha-amylase from ''Alicyclobacillus sp'', reveals accommodation of starch branching points in the alpha-amylase family]], Jon Agirre, Olga Moroz, Sebastian Meier, Jesper Brask, Astrid Munch, Tine Hoff, Carsten Andersen, Keith S. Wilsona and Gideon J. Davies
# [[Journal:Acta Cryst D:S2059798318015322|Structure of ISG15 from the bat species ''Myotis davidii'' and the impact of interdomain ISG15 interactions on viral protein engagement]], Caroline Langley, Octavia Goodwin, John V. Dzimianski, Courtney M. Daczkowski and Scott D. Pegan
# [[Journal:Acta Cryst D:S2059798318017047|The crystal structure of the N-acetylglucosamine 2-epimerase from ''Nostoc sp.'' KVJ10 reveals the true dimer]], Marie-Josee Haglund Halsør, Ulli Rothweiler, Bjørn Altermark and Inger Lin Uttakleiv Ræder
# [[Journal:Acta Cryst D:S2059798319000214|In-house high energy remote SAD-phasing using the magic triangle: how to tackle the P1 low symmetry using multiple orientations on the same human IBA57 crystal to increase multiplicity]], Spyridon Gourdoupis, Veronica Nasta, Simone Ciofi-Baffoni, Lucia Banci and Vito Calderone
# [[Journal:Acta Cryst D:S2059798319000676|Crystal structures of pyrrolidone-carboxylate peptidase I from ''Deinococcus radiodurans'' reveal the mechanism of L-pyroglutamate recognition]], Ravindra Makde
# [[Journal:Acta Cryst D:S2059798319002912|Crystal structure of the pseudoenzyme PDX1.2 in complex with its cognate enzyme PDX1.3]], Graham C. Robinson, Markus Kaufmann, Céline Roux, Jacobo Martinez-Font, Michael Hothorn, Stéphane Thore, and Teresa B. Fitzpatrick
# [[Journal:Acta Cryst D:S2059798319002304|The third structural switch in the molecule of archaeal translation initiation factor 2 and its possible role in initiation of GTP hydrolysis and removal of aIF2 from the ribosome]], Oleg Nikonov, Olesya Kravchenko, Natalia Nevskaya, Elena Stolboushkina, Maria Garber and Stanislav Nikonov
# [[Journal:Acta Cryst D:S2059798319006995|Structural insight into a matured humanized monoclonal antibody HuA21 against HER2-overexpressing cancer cells]], Zhenyi Wang, Liansheng Cheng, Gongrui Guo, Baoyun Cheng, Siyi Hu, Hongmin Zhang, Zhongliang Zhu and Liwen Niu
# [[Journal:Acta Cryst D:S2059798319007113|Crystal Structure Determination of ''Pseudomonas stutzeri'' A1501 endoglucanase Cel5A]], Raphael Dutoit, Maud Delsaute, Laetitia Collet, Corinne Vander Wauven, Dany Van Elder, Renaud Berlemont, Aurore Richel, Moreno Galleni and Cedric Bauvois
# [[Journal:Acta Cryst D:S2059798319004169|Structural and functional insights into phosphomannose isomerase]], Mamata Bangera, Giri Gowda K., S.R. Sagurthi and M.R.N. Murthy
# [[Journal:Acta Cryst D:S2059798319009008|Combining rMMS and the Magic Triangle for the efficient structure solution of a bacteriophage P68 lysin]], Jia Quyen Truong, Santosh Panjikar, Linda Shearwin, John Bruning and Keith Shearwin
# [[Journal:Acta Cryst D:S2059798319009574|Biochemical and structural explorations for α-hydroxyacid oxidases reveal a 4-electron oxidative decarboxylation reaction]], Yeh HW, Lin KH, Lyu SY, Li YS, Huang CM, Wang YL, Shih HW, Hsu NS, Wu CJ, Li TL
# [[Journal:Acta Cryst D:S2059798319011355|Comparison of a retroviral protease crystallized as a monomer and a dimer]], Stanislaw Wosicki, Miroslaw Gilski, Helena Zabranska, Iva Pichova, Mariusz Jaskolski
# [[Journal:Acta Cryst D:S2059798320003101|The crystal structure of heme ''d<sub>1</sub>'' biosynthesis-associated small c-type cytochrome NirC reveals mixed oligomeric states ''in crystallo'']], Thomas Klünemann, Steffi Henke and Wulf Blankenfeldt
# [[Journal:Acta Cryst D:S205979832000501X|A Baculoviral System for the Production of Human β-Glucocerebrosidase Enables Atomic Resolution Analysis]], Rhianna J. Rowland, Liang Wu, Feng Liu and Gideon J. Davies
# [[Journal:Acta Cryst D:S2059798320006841|A new modulated crystal structure of ANS complex of St John's wort Hyp-1 protein with 36 protein molecules in the asymmetric unit of the supercell]], Joanna Smietanska, Joanna Sliwiak, Miroslaw Gilski, Zbigniew Dauter, Radoslaw Strzalka, Janusz Wolny, Mariusz Jaskolski
# [[Journal:Acta Cryst D:S205979832000772X|Structural evidence for mono- and di-carboxylates binding at pharmacologically relevant extracellular sites of a pentameric ligand gated ion channel]], Zaineb Fourati, Ludovic Saugueta, and Marc Delarue
# [[Journal:Acta Cryst D:S2059798320008475|Getting the best of ID30B for RT data collection in microchips]], Jose A. Gavira, Isaac Rodriguez-Ruiz, Sergio Martinez-Rodriguez, Shibom Basu, Sébastien Teychené, Andrew A. McCarthy and Christoph Mueller-Dieckmann
# [[Journal:Acta Cryst D:S2059798320008116|Novel structure of the N-terminal helical domain of BibA, a Group B Streptococcus immunogenic bacterial adhesin]], Kartik Manne, Debasish Chattopadhyay, Vaibhav Agarwal, Anna M. Blom, Baldeep Khare, Srinivas Chakravarthy, Chungyu Chang, Hung Ton-That and Sthanam V. L. Narayana
# [[Journal:Acta Cryst D:S2059798320010906|Structure of CYRI-B / FAM49B, a key regulator of cellular actin assembly]], Elise Kaplan, Rachael Stone, Peter J. Hume, Nicholas P. Greene and Vassilis Koronakis
# [[Journal:Acta Cryst D:S2059798320011869|Lattice-translocation defects in some specific crystals of the catalytic head domain of influenza neuraminidase]], Linghui Li, Shuliu Dai, George F. Gao and Jiawei Wang
# [[Journal:Acta Cryst D:S205979832001253X|Structure of a GH51 α-L-arabinofuranosidase from ''Meripilus giganteus'': Conserved Substrate Recognition from Bacteria to Fungi]], Nicholas G.S. McGregor, Johan P. Turkenburg, Kristian B. R. Mørkeberg Krogh, Jens Erik Nielsen, Marta Artola, Keith A. Stubbs, Herman S. Overkleeft and Gideon J. Davies
# [[Journal:Acta Cryst D:S2059798320013510|Influence of the presence of the heme cofactor on the JK-loop structure in indoleamine-2,3-dioxygenase-1]], Mirgaux Manon, Leherte Laurence and Wouters Johan
# [[Journal:Acta Cryst D:S2059798320014540|Statistically correcting dynamical electron scattering improves refinement of protein nanocrystals, including charge refinement of coordinated metals]], Thorsten B. Blum, Dominique Housset, Max T.B. Clabbers, Eric van Genderen, Maria Bacia-Verloop, Ulrich Zander, Andrew A. McCarthy, Guy Schoehn, Wai Li Ling, Jan Pieter Abrahams
# [[Journal:Acta Cryst D:S205979832001517X|An engineered disulfide bridge traps and validates an outward-facing conformation in a bile acid transporter]], Xiaodong Wang, Ying Lyu, Yujia Ji, Ziyi Sun and Xiaoming Zhou
# [[Journal:Acta Cryst D:S2059798320015004|The substrate binding in the bile acid transporter ASBT<sub>Yf</sub> of ''Yersinia frederiksenii'']], Xiaodong Wang, Ying Lyu, Yujia Ji, Ziyi Sun and Xiaoming Zhou
# [[Journal:Acta Cryst D:S2059798321003922|Structure of the human factor VIIa/soluble tissue factor with calcium, magnesium and rubidium]], K. Vadivel, A. E. Schmidt, D. Cascio, K. Padmanabhan, S. Krishnaswamy, H. Brandstetter and S. P. Bajaj
# [[Journal:Acta Cryst D:S205979832100632X|Structure of the unique tetrameric STENOFOLIA homeodomain bound with promoter DNA]], Prabhat Kumar Pathak, Fei Zhang, Shuxia Peng, Lifang Niu, Juhi Chaturvedi, Justin Yoshida Elliott, Yan Xiang, Million Tadege, Junpeng Deng
# [[Journal:Acta Cryst D:S205979832100677X|A GH13 α-glucosidase from ''Weissella cibaria'' uncommonly acts on short-chain maltooligosaccharides]], Karan Wangpaiboon, Pasunee Laohawuttichai, Sun-Yong Kim, Tomoyuki Mori, Santhana Nakapong, Rath Pichyangkura, Piamsook Pongsawasdi, Toshio Hakoshima and Kuakarun Krusong
# [[Journal:Acta Cryst D:S2059798321006628|Structure of a C1/C4-oxidizing AA9 lytic polysaccharide monooxygenase from the thermophilic fungus ''Malbranchea cinnamomea'']], Scott Mazurkewich, Andrea Seveso, Silvia Hüttner, Gisela Brändén, Johan Larsbrink
# [[Journal:Acta Cryst D:S2059798321009633|Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family]], Marketa Soltysova, Irena Sieglova, Milan Fabry, Jirı Brynda, Jana Skerlova and Pavlına Rezacova
# [[Journal:Acta Cryst D:S2059798321008937|Structural and catalytic characterization of ''Blastochloris viridis'' and ''Pseudomonas aeruginosa'' homospermidine synthases supports the essential role of cation-''π'' interaction]], F. Helfrich and Axel J. Scheidig
# [[Journal:Acta Cryst D:S2059798322000948|A new inactive conformation of SARS-CoV-2 main protease]], Emanuele Fornasier, Maria Ludovica Macchia, Gabriele Giachin, Alice Sosic, Matteo Pavan, Mattia Sturlese, Cristiano Salata, Stefano Moro, Barbara Gatto, Massimo Bellanda and Roberto Battistutta
# [[Journal:Acta Cryst D:S2059798322002157|The X-ray crystallography phase problem solved thanks to AlphaFold and RoseTTAFold models: a case study report]], Irène Barbarin-Bocahu, Marc Graille
# [[Journal:Acta Cryst D:S2059798322001772|Crystal structure of the putative cell wall lipoglycan biosynthesis protein LmcA from ''Mycobacterium smegmatis'']], Onisha Patel, Rajini Brammananth, Weiwen Dai, Santosh Panjikar, Ross L. Coppel, Isabelle S. Lucet and Paul K. Crellin
# [[Journal:Acta Cryst D:S2059798322003928|Racemic crystal structures of A-DNA duplexes]], Pradeep K. Mandal, Gavin W. Collie, Brice Kauffmann and Ivan Huc
# [[Journal:Acta Cryst D:S2059798322004612|Structural Visualization of Transient Interactions Between the ''cis''-acting Acyltransferase and Acyl Carrier Protein of Salinomycin Modular Polyketide Synthase]], Y. Feng, F. Zhang, S. Huang, Z. Deng, L. Bai and J. Zheng
# [[Journal:Acta Cryst D:S2059798322007082|Native glycosylation and binding of the anti-depressant paroxetine in a low-resolution crystal structure of human myeloperoxidase]], Lucas Krawczyk, Shubham Semwal, Jalal Soubhye, Salma Lemri Ouadriri, Martine Prévost, Pierre Van Antwerpen, Goedele Roos, & Julie Bouckaert
# [[Journal:Acta Cryst D:S2059798322007677|Structural bases for the higher adherence to ACE2 conferred by the SARS-CoV-2 spike Q498Y substitution]], Elena Erausquin, Fabian Glaser, Juan Fernández-Recio, Jacinto López-Sagaseta
# [[Journal:Acta Cryst D:S2059798322008373|Structural basis for the transformation of traditional medicine berberine by bacterial nitroreductase]], Hai-Ying Wen, Li-Bin Pan, Shu-Rong Ma, Xin-Yu Yang, Jia-Chun Hu, Hai-Fan Zhao, Zeng-Qiang Gao, Yu-Hui Dong, Jian-Dong Jiang, Yan Wang and Heng Zhang
# [[Journal:Acta Cryst D:S2059798322009755|Structural and functional investigation of the human snRNP assembly factor AAR2 in complex with the PRPF8 RNaseH domain]], Marco Preussner, Karine F. Santos, Jonathan Alles, Christina Heroven, Florian Heyd, Markus C. Wahl, Gert Weber
# [[Journal:Acta Cryst D:S2059798322010762|Structure of a hydrophobic leucinostatin derivative determined by host lattice display.]], Cedric Kiss, Flavio M. Gall, Birgit Dreier, Michael Adams, Rainer Riedl, Andreas Plückthun and Peer R. E. Mittl
# [[Journal:Acta Cryst D:S2059798322011639|''Drosophila melanogaster'' Frataxin: Protein Crystal and Predicted Solution Structure with Identification of the Fe-Binding Regions]], Andria V. Rodrigues, Sharon Batelu, Tiara V. Hinton, John Rotondo, Lindsey Thompson, Joseph S. Brunzelle, Timothy L. Stemmler
# [[Journal:Acta Cryst D:S205979832201186X|Structures of permuted halves of a modern ribose binding protein]], Florian Michel, Sooruban Shanmugaratnam, Sergio Romero-Romero, Birte Höcker
# [[Journal:Acta Cryst D:S2059798323001936|Structures of L-proline trans-hydroxylase reveal the catalytic specificity and provide deeper insight into AKG-dependent hydroxylation]], Xiaoyan Hu, Xue Huang, Jiao Liu, Ping Zheng, Weimin Gong and Lin Yang
# [[Journal:Acta Cryst D:S2059798323004175|Structure-function studies of a novel laccase-like multicopper oxidase from ''Thermothelomyces thermophila'' provide insights into its biological role]], Christos Kosinas, Anastasia Zerva, Evangelos Topakas and Maria Dimarogona
# [[Journal:Acta Cryst D:S2059798323006642|Atypical Homodimerisation Revealed by the Structure of (S)-Enantioselective Haloalkane Dehalogenase DmmarA from ''Mycobacterium marinum'']], Karolina Snajdarova, Sérgio M. Marques, Jiri Damborsky, David Bednar, Martin Marek
# [[Journal:Acta Cryst D:S2059798323007672|The impact of molecular variants, crystallization conditions and the space group on ligand-protein complexes: A case study on bacterial phosphotriesterase]], Orly Dym, Nidhi Aggarwal, Yacov Ashani, Haim Leader, Shira Albeck, Tamar Unger, Shelly Hamer Rogotner, Israel Silman, Dan S. Tawfik and Joel L. Sussman
# [[Journal:Acta Cryst D:S2059798324001360|Characterization of novel mevalonate kinases from the tardigrade ''Ramazzottius varieornatus'' and the psychrophilic archaeon ''Methanococcoides burtonii'']], Lygie Esquirol, Janet Newman, Tom Nebl, Colin Scott, Claudia Vickers, Frank Sainsbury, Thomas S. Peat
# [[Journal:Acta Cryst D:S2059798324005229|Factors affecting macromolecule orientations in thin films formed in cryo-EM]], Swati Yadav and Vinothkumar Kutti Ragunath
# [[Journal:Acta Cryst D:S2059798324005461|Toward a dependable data set of structures for L-asparaginase]], Alexander Wlodawer, Zbigniew Dauter, Jacek Lubkowski, Joanna I. Loch, Dariusz Brzezinski, Miroslaw Gilski, Mariusz Jaskolski
# [[Journal:Acta Cryst D:S2059798324006594|Crystal structure of glycerol kinase from ''Trypanosoma cruzi'', a potential molecular target in Chagas disease]], Lipinski, Sonani & Dubin
# [[Journal:Acta Cryst D:S2059798324007733|Structural analysis of a ligand-triggered intermolecular disulfide switch in a major latex protein from opium poppy]], Samuel C. Carr, Peter J. Facchini, Kenneth K.S. Ng
# [[Journal:Acta Cryst D:S2059798324008246|Comparison of two crystal polymorphs of NowGFP reveals a new conformational state trapped by crystal packing]], Jin Kyun Kim<ref name="Paper_PMID">PMID:39222305</ref>, Hannah Jeong, Jeongwoo Seo, Seoyoon Kim, Kyung Hyun Kim, Duyoung Min, Chae Un Kim
# [[Journal:Acta Cryst D:S2059798324008210|Microcrystal electron diffraction structure of Toll-like-receptor 2 TIR domain-nucleated MyD88 TIR domain higher-order assembly]], Li, Pacoste, Gu, Thygesen, Stacey, Ve, Kobe, Xu, & Nanson
# [[Journal:Acta Cryst D:S205979832500292X|Unique double-helical packing of protein molecules in the crystal of K-independent L-asparaginase from common bean]], Dr Joanna Loch
# [[Journal:Acta Cryst D:S2059798325007065|Crystal structures of forty- and seventy-one-substitution variants of hydroxynitrile lyase from rubber tree]], Colin T. Pierce, Panhavuth Tan, Lauren R. Greenberg, Meghan E. Walsh, Ke Shi, Alana H. Nguyen, Elyssa L. Meixner, Sharad Sarak, Hideki Aihara, Robert L. Evans III, Romas J. Kazlauskas
# [[Journal:Acta Cryst D:S2059798325007089|Off-Target Structural Insights: ArnA and AcrB in Bacterial Membrane Protein Cryo-EM Analysis]], Mehmet Caliseki, Ufuk Borucu, Sathish K. N. Yadav, Christiane Schaffitzel and Burak Veli Kabasakal
# [[Journal:Acta Cryst D:S2059798325007673|Complex formation of Streptomyces griseolus CYP105A1 with statins by room-temperature crystal data collection]], Teisuke Takita, Sachiyo Yoneda, Kaori Yasuda, Kimihiko Mizutani, Kiyoshi Yasukawa, Toshiyuki Sakaki and Bunzo Mikami
# [[Journal:Acta Cryst D:S2059798326000422|Crystal structure of Schistosoma mansoni Cathepsin D1 in complex with a nanobody reveals the conformation of the propeptide bound state]], Professor Raymond J Owens
===Acta Cryst F ''Acta Crystallographica Section F''===
# [[Journal:Acta Cryst F:S1744309112003326|Structure of recombinant human carboxylesterase 1 isolated from whole cabbage looper larvae]], Harry M. Greenblatt, Tamara C. Otto, Melanie G. Kirkpatrick, Elena Kovaleva, Susan Brown, George Buchman, Douglas M. Cerasoli and Joel L. Sussman
# [[Journal:Acta Cryst F:S1744309112050270|Crystal structure of ADL1, a plant-specific homologue of the universal diaminopimelate amino transferase enzyme of lysine biosynthesis]], Vladimir Sobolev, Marvin Edelman, Orly Dym, Tamar Unger, Shira Albeck, Menny Kirma and Gad Galili
# [[Journal:Acta Cryst F:S2053230X18014814|Crystal structure and kinetic analyses of a hexameric form of (S)-3-hydroxybutyryl-CoA dehydrogenase from ''Clostridium acetobutylicum'']], Mihoko Takenoya, Seiichi Taguchi and Shunsuke Yajima
# [[Journal:Acta Cryst F:S2053230X18016217|The structure of ''Mycobacterium tuberculosis'' HtrA reveals an auto-regulatory mechanism]], Arvind Kumar Gupta, Debashree Behera and Balasubramanian Gopal
# [[Journal:Acta Cryst F:S2053230X18018083|An assessment of three human methylenetetrahydrofolate dehydrogenase/cyclohydrolase ligand complexes following further refinement]], Renata V. Bueno, Alice Dawson and William N. Hunter
# [[Journal:Acta Cryst F:S2053230X19000815|Crystal structure of Type VI immunity protein Tdi1 (Atu4351) from ''Agrobacterium tumefaciens'']], Lingling Shi, Zengqiang Gao, Tianyi Zhang, Heng Zhang and Yuhui Dong
# [[Journal:Acta Cryst F:S2053230X19001213|Substrate analogue complex structure of ''Mycobacterium tuberculosis'' decaprenyl diphosphate synthase]], Tzu-Ping Ko, Xiansha Xiao, Rey-Ting Guo, Jian-Wen Huang, Weidong Liu, Chun-Chi Chen
# [[Journal:Acta Cryst F:S2053230X19002693|Crystal structure of phosphoribulokinase from ''Synechococcus sp.'' strain PCC 6301]], Robert Wilson, Manajit Hayer-Hartl and Andreas Bracher
# [[Journal:Acta Cryst F:S2053230X19002863|Functional and structural characterization of IdnL7, an adenylation enzyme involved in incednine biosynthesis]], Jolanta Cieślak, Akimasa Miyanaga, Makoto Takaishi, Fumitaka Kudo, Tadashi Eguchi
# [[Journal:Acta Cryst F:S2053230X19004151|Phasing with calcium at home]], Shuaiqi Guo, Robert Campbell, Peter L. Davies and John S. Allingham
# [[Journal:Acta Cryst F:S2053230X19004618|Novel T9 loop interaction of Filamenting Temperature-sensitive mutant Z from ''Mycobacterium tuberculosis'']], E. O. Lazo, J. Jakoncic, S. RoyChowdhury, D. Awasthi, I. Ojima
# [[Journal:Acta Cryst F:S2053230X19004424|Structure of the Ebola virus nucleoprotein - RNA complex]], Robert N. Kirchdoerfer, Erica Ollmann Saphire, Andrew B. Ward
# [[Journal:Acta Cryst F:S2053230X19007192|Crystal Structure of Flavin Dependent Thymidylate Synthase, Thy1, from ''Thermus thermophilus'' having an Extra C Terminal Domain]], A. Ogawa, G. Sampei and G. Kawai
# [[Journal:Acta Cryst F:S2053230X20000199|Structure of MP-4 from ''Mucuna pruriens'' at 2.22 Å resolution]], Abha Jain, Amit Kumar, Meha Shikhi, Ashish Kumar, Deepak T. Nair and Dinakar M. Salunke
# [[Journal:Acta Cryst F:S2053230X20002988|Structural characterization of the human O-phosphoethanolamine phospho-lyase]], Chiara Vettraino, Alessio Peracchi, Stefano Donini, Emilio Parisini
# [[Journal:Acta Cryst F:S2053230X20004343|Structure of ''Mycobacterium smegmatis'' α-maltose-1-phosphate synthase GlgM]], Karl Syson, Clare E. M. Stevenson, David M. Lawson and Stephen Bornemann
# [[Journal:Acta Cryst F:S2053230X20010122|Crystal structure of the extracellular domain of the receptor-like kinase TMK3 from ''Arabidopsis thaliana'']], Hong Chen, Yanqiong Kong, Jia Chen, Lan Li, Xiushan Li, Feng Yu, Zhenhua Ming
# [[Journal:Acta Cryst F:S2053230X20011310|Crystallization and structure of ebselen bound to cysteine 141 of human inositol monophosphatase (IMPase).]], Gareth D. Fenn, Helen Waller-Evans, John R. Atack and Benjamin D. Bax
# [[Journal:Acta Cryst F:S2053230X20011309|Multiple crystal forms of human MacroD2]], Sarah Wazir, Mirko M. Maksimainen and Lari Lehtiö
# [[Journal:Acta Cryst F:S2053230X20010237|High-resolution structure of alcohol dehydrogenase from the bifunctional bacterial enzyme AdhE]], Liyana Azmi, Eilis C. Bragginton, Ian T. Cadby, Olwyn Byron, Andrew J. Roe, Andrew L. Lovering and Mads Gabrielsen
# [[Journal:Acta Cryst F:S2053230X20016015|Using Yeast Surface Display to Engineer a Soluble and Crystallizable Construct of HPK1]], Wai L. Lau, Bradley Pearce, Heather Malakian, Iyoncy Rodrigo, Dianlin Xie, Mian Gao, Frank Marsilio, Chiehying Chang, Max Ruzanov, Jodi K. Muckelbauer, John A. Newitt, Dasa Lipovsek and Steven Sheriff
# [[Journal:Acta Cryst F:S2053230X21008761|Complex structure of acyltransferase VinK and carrier protein VinL with a pantetheine cross-linking probe]], Akimasa Miyanaga, Risako Ouchi, Fumitaka Kudo and Tadashi Eguchi
# [[Journal:Acta Cryst F:S2053230X21008542|Glycogen phosphorylase revisited: extending the resolution of the R- and T-state structures of the free enzyme and in complex with allosteric activators]], Demetres D. Leonidas, Spyros E. Zographos, Katerina E. Tsitsanou, Vasiliki T. Skamnaki, George Stravodimos, and Efthimios Kyriakis
# [[Journal:Acta Cryst F:S2053230X21008967|Microcrystal preparation for serial femtosecond X-ray crystallography of bacterial copper amine oxidase]], Takeshi Murakawa, Mamoru Suzuki, Toshi Arima, Michihiro Sugahara, Tomoyuki Tanaka, Rie Tanaka, So Iwata, Eriko Nango, Kensuke Tono, Hideyuki Hayashi, Kenji Fukui, Takato Yano, Katsuyuki Tanizawa, and Toshihide Okajima
# [[Journal:Acta Cryst F:S2053230X21013455|Crystal structure of betaine aldehyde dehydrogenase from ''Burkholderia pseudomallei'']], Dylan K. Beard, Sandhya Subramanian, Jan Abendroth, Thomas E. Edwards, Peter J. Myler, and Oluwatoyin A. Asojo
# [[Journal:Acta Cryst F:S2053230X21012632|Crystal structure of a putative short-chain dehydrogenase/reductase from ''Paraburkholderia xenovorans'']], Jayson Davidson, Kyndall Nicholas, Jeremy Young, Deborah G. Conrady, Stephen Mayclin, Sandhya Subramanian, Bart L. Staker, Peter J. Myler and Oluwatoyin A. Asojo
# [[Journal:Acta Cryst F:S2053230X21013595|Crystal structure of a hypothetical protein from ''Giardia lamblia'']], Dylan Beard, Seonna Bristol, Kayla Cosby, Amber Davis, Courtney Manning, Lionel Perry, Lauren Snapp, Arian Toy, Kayla Wheeler, Jeremy Young, Bart L Staker, David Dranow, Jan Abendroth, Sandhya Subramanian, Thomas E Edwards, Peter J Myler, and Oluwatoyin A. Asojo
# [[Journal:Acta Cryst F:S2053230X22002448|Structure and activity of a thermally stable mutant of Acanthamoeba Actophorin]], Stephen Quirk and Raquel Lieberman
# [[Journal:Acta Cryst F:S2053230X22006586|Crystal structure determination of the halogenase CtcP from ''Streptomyces aureofaciens'']], Lijuan Yin
# [[Journal:Acta Cryst F:S2053230X22007555|Crystal structures of glutamyl-tRNA synthetase from ''Elizabethkingia anopheles'' and ''E. meningosepticum'']], Lauryn Brooks, Sandhya Subramanian, David M. Dranow, Stephen J. Mayclin, Peter J. Myler, and Oluwatoyin A. Asojo
# [[Journal:Acta Cryst F:S2053230X23003801|Bacterial Structural Genomics Target Enabled by Recently Discovered Potent Fungal ACS Inhibitor]], Nicholas D. DeBouver, Madison J. Bolejack, Taiwo E. Esan, Damian J. Krysan, Timothy J. Hagen, Jan Abendroth
# [[Journal:Acta Cryst F:S2053230X23004430|Crystal structure of thermostable acetaldehyde dehydrogenase from the hyperthermophilic archaeon, ''Sulfolobus tokodaii'']], Shohei Mine, Makoto Nakabayashi and Kazuhiko Ishikawa
# [[Journal:Acta Cryst F:S2053230X23006817|Drastic alterations in the loop structure around colchicine upon complex formation with an engineered lipocalin indicate a conformational selection mechanism]], Elena Jerschke, Andreas Eichinger and Arne Skerra
# [[Journal:Acta Cryst F:S2053230X24003911|Structural and biochemical characterization of the M405S variant of ''Desulfovibrio vulgaris'' formate dehydrogenase]], Guilherme Vilela-Alves, Rita Rebelo Manuel, Neide Pedrosa, Ines A. Cardoso Pereira, Maria Joao Romao and Cristiano Mota
# [[Journal:Acta Cryst F:S2053230X24004655|Cryo-EM structure and functional analysis of chromatin remodeler RSF]], Jiale Zhang, Heyu Zhao, Binqian Zou, Huadong Li, Shuqi Dong, Jiali Guan, Chi Wang, Weijie Li, Yutong Liu, Yingying Chen, Nadia Rasheed and Jun He
# [[Journal:Acta Cryst F:S2053230X24008604|Ternary structure of ''Plasmodium vivax N''-myristoyltransferase with myristoyl-CoA and inhibitor IMP-0001173]], Bolling, Mendez, Taylor, Makumire, Reers, Zigweid, Subramanian, Dranow, Staker, Edwards, Tate, Bell, Myler, Asojo & Chakafana
# [[Journal:Acta Cryst F:S2053230X24010094|Human TGFβR1 in complex with kinase inhibitor SB505124]], Jhon A. Rodriguez Buitrago, Marene Landstrom, Magnus Wolf-Watz
# [[Journal:Acta Cryst F:S2053230X24011099|Crystal structure of glutamyl-tRNA synthetase from H''elicobacter pylori'']], Dr Oluwatoyin A. Asojo
# [[Journal:Acta Cryst F:S2053230X24012056|Co-crystal structure of ''Helicobacter pylori'' biotin acetyl-CoA carboxylase synthetase (biotin protein ligase) with biotinyl-5-ATP]], Jesuferanmi P. Ayanlade, Dylan E. Davis, Sandhya Subramanian, David Dranow, Donald D. Lorimer, Brad Hammerson, Peter J. Myler, and Oluwatoyin A. Asojo
# [[Journal:Acta Cryst F:S2053230X25002298|Structures of M. tuberculosis Rv2173 isoprenyl diphosphate synthase in substrate-bound forms]], James A. Titterington, Ngoc Anh Thu Ho, Charles P.H. Beasley, Francis Mann, Edward N. Baker, Timothy M. Allison, Jodie M. Johnston
# [[Journal:Acta Cryst F:S2053230X25003905|Crystal structure of a recombinant mushroom Agaricus bisporus mannose-binding protein with a longer C-terminal region]], Dr Hiromi Yoshida
# [[Journal:Acta Cryst F:S2053230X25005254|Structural plasticity of human Fascin1: A target for cancer treatment]], Dr Jose Manuel Martin-Garcia
# [[Journal:Acta Cryst F:S2053230X25007034|Crystal structure of a seven-substitution mutant of hydroxynitrile lyase from rubber tree]], Colin T. Pierce, Lauren R. Greenberg, Meghan E. Walsh, Ke Shi, Drenen J. Mageea, Hideki Aihara, Wendy Gordon, Robert L. Evans III and Romas J. Kazlauskas
# [[Journal:Acta Cryst F:S2053230X25006181|The structures of Listeria monocytogenes MenD in ThDP-bound and in-crystallo captured intermediate I-bound forms]], Michelle Bailey, Fiona M. Given, Ngoc Anh Thu Ho, F. Grant Pearce, Timothy M. Allison and Jodie M. Johnston
===Angew Chem Int Ed ''''===
# [[Journal:Angew Chem Int Ed:1|Fine tuning of chlorophyll spectra by protein-induced ring deformation]], Dominika Bednarczyk, Orly Dym, Yoav Peleg, Vadivel Prabahar, and Dror Noy
===BAMBEd ''Biochemistry and Molecular Biology Education''===
# [[Journal:BAMBEd:Acetylcholinesterase: Substrate Traffic and Inhibition|Acetylcholinesterase: Substrate traffic and inhibition]], Mary G. Acheampong, Daviana E. Dueño, Bobby K. Glover, Alafia A. Henry, Randol Mata, Marisa L. VanBrakle, Lars F. Westblade, Joel L. Sussman, Allison L. Granberry
# [[Journal:BAMBEd:Citrate Synthase|Citrate Synthase]], Wayne A. Decatur, Daniel B. Eddelman
# [[Journal:BAMBEd:How do we get the oxygen we breathe|Tutorial: How we get the oxygen we breathe]], Jaime Prilusky, Eran Hodis
# [[Journal:BAMBEd:Beta-prime subunit of bacterial RNA polymerase|Beta‐prime subunit of bacterial RNA polymerase]], Catherine Louise Dornfeld, Mark Hoelzer, Steven Forst
# [[Journal:BAMBEd:Deoxyribonucleic Acid (DNA)|Deoxyribonucleic Acid (DNA)]], Adithya Sagar, Karl Oberholser
# [[Journal:BAMBEd:Mammalian serine hydrolases|Mammalian serine hydrolases]], R. Jeremy Johnson, Andrew Bartels, Rachel Erkilla, Nicole Green, Steven Han Nathaniel Holt Melissa Jones Daniel Lange Kelly Maddalone Joshua Morris Ryan Mughmaw Derek O'Connor Nicole Risselmann Carter Sharp Dominique Stephens Audrey Wright Erica Yothment Gregory Zemtsov
# [[Journal:BAMBEd:Eukaryotic Protein Kinase Catalytic Domain|Eukaryotic Protein Kinase Catalytic Domain]], Alice C. Harmon
# [[Journal:BAMBEd:G-protein coupled receptors|G‐protein coupled receptors]], R. Jeremy Johnson, Jacob Applegarth Steven Bennett Sydney Caskey Connor Coatney Kurt Corsbie Allison Cotter Daniel Cotter Alexis Coulis Heather Hansen Whitney Hart Cutter Koehler Andrew Koelper Stephanie Kuhlman Chandler Mitchell Blake Moskal Olivia Murfield Allie Paton Daniel Schemenauer Brittany Stankavich Clayton Taylor Brent Waibel L. Dean Williams
# [[Journal:BAMBEd:HMG-CoA reductase|HMG‐CoA reductase]], David Canner
# [[Journal:BAMBEd:3D visualization and annotation of transcription factor-DNA readout modes|3D visualization and annotation of transcription factor–DNA readout modes]], Ana Carolina Dantas Machado, Skyler B. Saleebyan, Bailey T. Holmes, Maria Karelina, Julia Tam, Sharon Y. Kim, Keziah H. Kim, Iris Dror, Eran Hodis, Eric Martz, Patricia A. Compeau, Remo Rohs
# [[Journal:BAMBEd:Coiled-coil structure of keratins|Coiled‐coil structure of keratins]], Israel Hanukoglu, Liora Ezra
# [[Journal:BAMBEd:The large ribosomal subunit of Haloarcula marismortui|The large ribosomal subunit of ''Haloarcula marismortui'']], Wayne A. Decatur
# [[Journal:BAMBEd:Bovine pancreatic ribonuclease a|Bovine pancreatic ribonuclease a]], R. Jeremy Johnson, Mary Andorfer, Ashton Chaffee, Melanie Clark, Nathan Clarke, Grace Douglass, Elizabeth Ellis, Emily Fischer, Carissa Fuller, Lauren Garnett, Lexi Gehring, Laurel Heckman, Daniel Kroupa, Lin Liu, Deanna Proimos, Micah Raebel, Kristyn Shaw, Michael Slack, Diana Trautmann, Ben Trefilek
# [[Journal:BAMBEd:Phosphoinositide 3-kinase|Phosphoinositide 3‐kinase]], David Canner
# [[Journal:BAMBEd:Ramachandran plots|Ramachandran plots]], Karl Oberholser
# [[Journal:BAMBEd:A practical guide to teaching with Proteopedia|A practical guide to teaching with Proteopedia]], Claudia Castro, R. Jeremy Johnson, Bruno Kieffer, John A. Means, Ann Taylor, Jason Telford, Lynmarie K. Thompson, Joel L. Sussman, Jaime Prilusky, Karsten Theis
# [[Journal:BAMBEd:Triose Phosphate Isomerase|Triose Phosphate Isomerase]], Gregg W. Snider
# [[Journal:BAMBEd:Ricin|Ricin]], Ann Taylor
# [[Journal:BAMBEd:Rossmann fold: A beta-alpha-beta fold at dinucleotide binding sites|Rossmann fold: A beta-alpha-beta fold at dinucleotide binding sites]], Israel Hanukoglu
===BMC ''Bioorganic & Medicinal Chemistry''===
# [[Journal:BMC:3|Identification of novel isocytosine derivatives as xanthine oxidase inhibitors from a set of virtual screening hits]], Chandrika B-Rao, Asha Kulkarni-Almeida, Kamlesh V. Katkar, Smriti Khanna, Usha Ghosh, Ashish Keche, Pranay Shah, Ankita Srivastava, Vaidehi Korde, Kumar V. S. Nemmani, Nitin J. Deshmukh, Amol Dixit, Manoja K. Brahma, Umakant Bahirat, Lalit Doshi, Rajiv Sharma, H. Sivaramakrishnan
===CHEMBIOINT ''Chemico-Biological Interactions''===
# [[Journal:CHEMBIOINT:1|The four-helix bundle in cholinesterase dimers: structural and energetic determinants of stability]], Dana A. Novichkova, Sofya V. Lushchekina, Orly Dym, Patrick Masson, Israel Silman and Joel L. Sussman
# [[Journal:CHEMBIOINT:2|Molecular Dynamics Simulations of the Interaction of Mouse and ''Torpedo'' Acetylcholinesterase with Covalent Inhibitors Explain Their Differential Reactivity: Implications for Drug Design]], Nellore Bhanu Chandar, Irena Efremenko, Israel Silman, Jan M. L. Martin, and Joel L. Sussman
===Cell ===
# [[Journal:Cell:1|Structural linkage between ligand discrimination and receptor activation by type I interferons]], Christoph Thomas, Ignacio Moraga, Doron Levin, Peter O. Krutzik, Yulia Podoplelova, Angelica Trejo, Choongho Lee, Ganit Yarden, Susan E. Vleck, Jeffrey S. Glenn, Garry P. Nolan, Jacob Piehler, Gideon Schreiber, K. Christopher Garcia
===FEBS Journal ===
# [[Journal:FEBS Journal:1|Flexible regions govern promiscuous binding of IL-24 to receptors IL-20R1 and IL-22R1]], Jiří Zahradník, Lucie Kolářová, Yoav Peleg, Petr Kolenko, Silvie Svidenská, Tatsiana Charnavets, Tamar Unger, Joel L. Sussman, and Bohdan Schneider
===FEBS Open Bio ===
# [[Journal:FEBS Open Bio:1|Crystal structure of the essential biotin-dependent carboxylase AccA3 from ''Mycobacterium tuberculosis'']], Matthew Bennett, Martin Högbom
# [[Journal:FEBS Open Bio:2|Structural evidence for Arabidopsis glutathione transferase AtGSTF2 functioning as a transporter of small organic ligands]], Laziana Ahmad, Elizabeth L. Rylott, Neil C. Bruce, Robert Edwards and Gideon Grogan
===FLS ''Frontiers in Life Science''===
# [[Journal:FLS:1|Crystal structure of porcine pancreatic phospholipase A<sub>2</sub> in complex with 2-methoxycyclohexa-2-5-diene-1,4-dione]], K. V. Dileep, I. Tintu, P. K. Mandal, P. Karthe, M. Haridas and C. Sadasivan
===Genes ===
# [[Journal:Genes:1|A DNA Structural Alphabet Distinguishes Structural Features of DNA Bound to Regulatory Proteins and in the Nucleosome Core Particle]], Bohdan Schneider, Paulina Bozikova, Petr Cech, Daniel Svozil and Jiri Cerny
===IUCrJ ===
# [[Journal:IUCrJ:S2052252518018274|A cytosine modification mechanism revealed by the ternary complex structure of deoxycytidylate hydroxymethylase from bacteriophage T4 with its cofactor and substrate]], Si Hoon Park, Se Won Suh and Hyun Hyu Song
# [[Journal:IUCrJ:S2052252519001568|Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition]], Anna Cuppari, Hagen Körschgen, Dirk Fahrenkamp, Carlo Schmitz, Tibisay Guevara, Konstantin Karmilin, Michael Kuske, Mario Olf, Eileen Dietzel, Irene Yiallouros, Daniele de Sanctis, Theodoros Goulas, Ralf Weiskirchen, Willi Jahnen-Dechent, Julia Floehr, Walter Stöcker, Luca Jovine and F. Xavier Gomis-Rüth
# [[Journal:IUCrJ:S2052252519002926|Determination of the Molecular Basis for Coprogen Import by Gram Negative Bacteria]], Rhys Grinter and Trevor Lithgow
# [[Journal:IUCrJ:S2052252519005761|Room-temperature photo-induced martensitic transformation in a protein crystal]], Steven Dajnowicz, Patricia S. Langan, Kevin L. Weiss, Ilia N. Ivanov, and Andrey Kovalevsky
# [[Journal:IUCrJ:S2052252519005372|The structural characterisation of a glucosylglycerate hydrolase provides insights into the molecular mechanism of mycobacterial recovery from nitrogen starvation]], Tatiana Barros Cereija, Susana Alarico, Eva C. Lourenço, José António Manso, M. Rita Ventura, Nuno Empadinhas, Sandra Macedo-Ribeiro and Pedro José Barbosa Pereira
# [[Journal:IUCrJ:S205225251901707X|Structural insights into conformational switching in latency-associated peptide between TGFβ-1 bound and unbound states]], Timothy R. Stachowski, Mary E. Snell, and Edward H. Snell
# [[Journal:IUCrJ:S205225252000072X|Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals]], Alexander M. Wolff, Iris D. Young, Raymond G. Sierra, Aaron S. Brewster, Michael W. Martynowycz, Eriko Nango, Michihiro Sugahara, Takanori Nakane, Kazutaka Ito, Andrew Aquila, Asmit Bhowmik, Justin T. Biel, Sergio Carbajo, Aina E. Cohen, Saul Cortez, Ana Gonzalez, Tomoya Hino, Dohyun Im, Jake D. Koralek, Minoru Kubo, Tomas S. Lazarou, Takashi Nomura, Shigeki Owada, Avi J. Samelson, Tomoyuki Tanaka, Rie Tanaka, Erin M. Thompson, Henry van den Bedem, Rahel A. Woldeyes, Fumiaki Yumoto, Wei Zhao, Kensuke Tono, Sébastien Boutet, So Iwata, Tamir Gonen, Nicholas K. Sauter, James S. Fraser, Michael C. Thompson
# [[Journal:IUCrJ:S2052252520001840|Structure of the MICU1-MICU2 heterodimer provides insights into the gatekeeping threshold shift]], Jongseo Park, Youngjin Lee, Taein Park, Jung Youn Kang, Sang A. Mun, Minwoo Jin, Jihyeong Yang and Soo Hyun Eom
# [[Journal:IUCrJ:S2052252520005709|Structural Definition of Polyspecific Compensatory Ligand Recognition by P-glycoprotein]], Christina A. Le, Daniel S. Harvey and Stephen G. Aller
# [[Journal:IUCrJ:S2052252520011008|Structural insights into the effect of active site mutation on carbonic anhydrase catalytic mechanism]], Jin Kyun Kim, Cheol Lee, Seon Woo Lim, Jacob T. Andring, Aniruddha Adhikari, Robert McKenna and Chae Un Kim
# [[Journal:IUCrJ:S2052252521005340|X-ray crystallography studies of RoAb13 bound to PIYDIN, a part of the CCR5 N-terminal domain]], Lata Govada, Emmanuel Saridakis, Sean C. Kassen, Ahmad Bin-Ramzi, Rhodri Marc Morgan, Benjamin Chain, John R. Helliwell and Naomi E. Chayen
# [[Journal:IUCrJ:S2052252521008125|Observation of Substrate Diffusion and Ligand Binding in Enzyme Crystals using High Repetition Rate Mix-and-Inject Serial Crystallography]], Suraj Pandey, George Calvey, Andrea M. Katz, Tek Narsingh Malla, Faisal H. M. Koua, Jose M. Martin-Garcia, Ishwor Poudyal, Jay-How Yang, Mohammad Vakili, Oleksandr Yefanov, Kara A. Zielinski, Saša Bajt, Salah Awel, Katerina Dörner, Matthias Frank, Luca Gelisio, Rebecca Jernigan, Henry Kirkwood, Marco Kloos, Jayanath Koliyadu, Valerio Mariani, Mitchell D. Miller, Grant Mills, Garrett Nelson, Jose L. Olmos Jr., Alireza Sadri, Tokushi Sato, Alexandra Tolstikova, Weijun Xu, Abbas Ourmazd, John H. C. Spence, Peter Schwander, Anton Barty, Henry N. Chapman, Petra Fromme, Adrian P. Mancuso, George N. Phillips Jr., Richard Bean, Lois Pollack, Marius Schmidt
# [[Journal:IUCrJ:S2052252521011696|Crystal structures of PigF, an O-methyltransferase involved in prodigiosin-synthetic pathway, reveal an induce-fit substrates recognition mechanism]], Shenshen Qiu, Dongqing Xu, Mengxue Xu, Huan Zhou, Ning Sun, Li Zhang, Mengmeng Zhao, Jianhua He, Tingting Ran, Bo Sun and Weiwu Wang
# [[Journal:IUCrJ:S2052252522007497|The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (Mpro)]], Ali Ebrahim, Blake T. Riley, Desigan Kumaran, Babak Andi, Martin R. Fuchs, Sean McSweeneyd, and Daniel A. Keedy
# [[Journal:IUCrJ:S2052252522006820|Organism Specific Differences in Binding of Ketoprofen to Serum Albumin]], Mateusz P. Czub, Alan J. Stewart, Ivan G. Shabalin, and Wladek Minor
# [[Journal:IUCrJ:S2052252524001969|The ABC Toxin Complex from ''Yersinia entomophaga'' Can Package a Cytotoxin Expressed from an “Orphan” Genetic Locus: the Structures of Both the RHS Shell and its Cargo.]], Jason N. Busby, Sarah Trevelyan, Cassandra L. Pegg, Edward D. Kerr, Benjamin L. Schulz, Irene Chassagnon, Michael J. Landsberg, Mitchell K. Weston, Mark R. H. Hurst, and J. Shaun Lott
# [[Journal:IUCrJ:S2052252524004627|From X-ray crystallographic structure to intrinsic thermodynamics of protein–ligand binding using carbonic anhydrase isozymes as a model system]], Vaida Paketuryte-Latve, Alexey Smirnov, Elena Manakova, Lina Baranauskiene, Vytautas Petrauskas, Asta Zubriene, Jurgita Matuliene, Virginija Dudutiene, Edita Capkauskaite, Audrius Zaksauskas, Janis Leitans, Saulius Grazulis, Kaspars Tars and Daumantas Matulis
# [[Journal:IUCrJ:S2052252524010170|Crystal structure of a bacterial photoactivated adenylate cyclase determined at room temperature by serial femtosecond crystallography]], Kapetanaki SM, Coquelle N, von Stetten D, Byrdin M, Rios-Santacruz R, Bean R, Bielecki J, Boudjelida M, Fekete Z, Grime GW, Han H, Hatton C, Kantamneni S, Kharitonov K, Kim C, Kloos M, Koua FHM, de Diego Martinez I, Melo D, Rane L, Round A, Round E, Sarma A, Schubert R, Schulz J, Sikorski M, Vakili M, Valerio J, Vitas J, de Wijn R, Wrona A, Zala N, Pearson A, Dörner K, Schirò G, Garman EF, Lukács A, Weik M.
# [[Journal:IUCrJ:S2052252525006645|Time-resolved serial synchrotron and serial femtosecond crystallography of heme proteins using photocaged nitric oxide]], Peter Smyth, Sofia Jaho, Lewis J. Williams, Gabriel Karras, Ann Fitzpatrick, Amy J. Thompson,a Sinan Battah, Danny Axford, Sam Horrell, Marina Lučić, Kotone Ishihara, Machika Kataoka, Hiroaki Matsuura, Kanji Shimba, Kensuke Tono, Takehiko Tosha, Hiroshi Sugimoto, Shigeki Owada, Michael A. Hough, Jonathan A.R. Worrall, Robin L. Owen
===JBIC ''Journal of Biological Inorganic Chemistry''===
# [[Journal:JBIC:1|Crystal structure of the zinc, cobalt and iron containing adenylate kinase from ''Desulfovibrio gigas'': a novel metal containing adenylate kinase from Gram-negative bacteria]], A. Mukhopadhyay, A.V. Kladova, S.A. Bursakov, O. Yu. Gavel, J.J. Calvete, V.L. Shnyrov, I. Moura, J.J.G. Moura, M.J. Romão, J. Trincão
# [[Journal:JBIC:2|Structure of Anticancer Ruthenium Half-Sandwich Complex Bound to Glycogen Synthase Kinase 3ß]], G. Atilla-Gocumen, L. Di Costanzo, E. Meggers
# [[Journal:JBIC:4|Bacterial ferrochelatase turns human: Tyr13 determines the apparent metal specificity of ''Bacillus subtilis'' ferrochelatase]], Mattias D. Hansson • Tobias Karlberg • Christopher A. G. So ̈derberg • Sreekanth Rajan • Martin J. Warren • Salam Al-Karadaghi • Stephen E. J. Rigby • Mats Hansson
# [[Journal:JBIC:0|TITLE]], AUTHORS
# [[Journal:JBIC:3|Structural characterization of human S100A16, a low-affinity calcium binder]], Elena Babini • Ivano Bertini • Valentina Borsi • Vito Calderone • Xiaoyu Hu • Claudio Luchinat • Giacomo Parigi
# [[Journal:JBIC:5|A Hyperactive Cobalt-Substituted Extradiol-Cleaving Catechol Dioxygenase]], Andrew J. Fielding, Elena G. Kovaleva, Erik R. Farquhar, John D. Lipscomb and Lawrence Que
# [[Journal:JBIC:6|Sco Proteins are Involved in Electron Transfer Processes]], Lucia Banci, Ivano Bertini, Simone Ciofi-Baffoni, Tatiana Kozyreva, Mirko Mori and Shenlin Wang
# [[Journal:JBIC:7|Structural and kinetic studies of imidazole binding to two members of the cytochrome c6 family reveal an important role for a conserved heme pocket residue]], Badri S. Rajagopal, Michael T. Wilson, Derek S. Bendall, Christopher J. Howe and Jonathan A.R. Worrall
# [[Journal:JBIC:8|A hydrogen-bonding network formed by the B10-E7-E11 residues of a truncated hemoglobin from Tetrahymena pyriformis is critical for stability of bound oxygen and nitric oxide detoxification]], Jotaro Igarashi, Kazuo Kobayashi and Ariki Matsuoka
# [[Journal:JBIC:9|Protein and metal cluster structure of the wheat metallothionein domain γ-Ec-1. The second part of the puzzle.]], Jens Loebus, Estevão A. Peroza, Nancy Blüthgen, Thomas Fox, Wolfram Meyer Klaucke, Oliver Zerbe and Eva Freisinger
# [[Journal:JBIC:10|Crystal structures of the all cysteinyl coordinated D14C variant of ''Pyrococcus furiosus'' ferredoxin: [4Fe-4S] <-> [3Fe-4S] cluster conversion]], Monika Nøhr Løvgreen, Maja Martic, Michael S. Windahl, Hans E. M. Christensen and Pernille Harris
# [[Journal:JBIC:11|{{nowrap|A Cryo-Crystallographic}} Time Course for Peroxide Reduction by Rubrerythrin from ''Pyrococcus furiosus'']], Bret Dillard, Jonathan Demick, Michael Adams and William Lanzilotta
# [[Journal:JBIC:12|ISC-like [2Fe-2S] ferredoxin (FdxB) dimer from ''Pseudomonas putida'' JCM 20004: Structural and electron nuclear double resonance characterization]], Toshio Iwasaki, Reinhard Kappl, Gerhard Bracic, Nobutaka Shimizu, Daijiro Ohmori and Takashi Kumasaka
# [[Journal:JBIC:13|{{nowrap|N-Butylisocyanide Oxidation}} at the {{nowrap|[NiFe<sub>4</sub>S<sub>4</sub>OH<sub>x</sub>]-cluster}} of CO Dehydrogenase]], Jae-Hun Jeoung and Holger Dobbek
# [[Journal:JBIC:14|Multifaceted SlyD from ''Helicobacter pylori'': implication in [NiFe] hydrogenase maturation]], Tianfan Cheng, Hongyan Li, Wei Xia and Hongzhe Sun
# [[Journal:JBIC:15|Potent Inhibition of Dinuclear Zinc(II) Peptidase, an Aminopeptidase from Aeromonas proteolytica, by 8-Quinolinol Derivatives: Inhibitor Design Based on Zn2+ Fluorophores, Kinetic, and X-ray Crystallographic Study]], Kengo Hanaya, Miho Suetsugu, Shinya Saijo, Ichiro Yamato, and Shin Aoki
# [[Journal:JBIC:16|Laue Crystal Structure of ''Shewanella oneidensis'' Cytochrome c Nitrite Reductase from a High-yield Expression System]], Matthew Youngblut, Evan T. Judd, Vukica Srajer, Bilal Sayyed, Tyler Goelzer, Sean J. Elliott, Marius Schmidt and A. Andrew Pacheco
# [[Journal:JBIC:17|Peptidylglycine α-Hydroxylating Monooxygenase (PHM)-coordination of peroxide to Cu<sub>M</sub> center. Structural and computational study]], Katarzyna Rudzka, Diego M. Moreno, Betty Eipper, Richard Mains, Dario A. Estrin and L. Mario Amzel,
# [[Journal:JBIC:18|Solution structure and dynamics of human S100A14]], Ivano Bertini, Valentina Borsi, Linda Cerofolini, Soumyasri Das Gupta, Marco Fragai and Claudio Luchinat
# [[Journal:JBIC:19|Heterometallic [AgFe<sub>3</sub>S<sub>4</sub>] ferredoxin variants – synthesis, characterization and the first crystal structure of an engineered heterometallic iron-sulfur protein]], Maja Martic, Ida Noémi Jakab-Simon, Lærke Tvedebrink Haahr, Wilfred Raymond Hagen and Hans Erik Mølager Christensen
# [[Journal:JBIC:20|The crystal structure of ''Sporosarcina pasteurii'' urease in a complex with citrate provides new hints for inhibitor design]], Stefano Benini, Paulina Kosikowska, Michele Cianci, Luca Mazzei, Antonio Gonzalez Vara, Łukasz Berlicki, and Stefano Ciurli
# [[Journal:JBIC:21|The mechanism of copper uptake by tyrosinase from ''Bacillus megaterium'']], Margarita Kanteev, Mor Goldfeder, Michał Chojnacki, Noam Adir, and Ayelet Fishman
# [[Journal:JBIC:22|The crystal structure of an extracellular catechol oxidase from the ascomycete fungus <i>Aspergillus oryzae</i>]], Nina Hakulinen, Chiara Gasparetti, Heidi Kaljunen, Kristiina Kruus, and Juha Rouvinen
# [[Journal:JBIC:23|Selectivity of Ni(II) and Zn(II) binding to ''Sporosarcina pasteurii'' UreE, a metallo-chaperone in the urease assembly: a calorimetric and crystallographic study]], Barbara Zambelli, Katarzyna Banaszak, Anna Merloni, Agnieszka Kiliszek, Wojciech Rypniewski, Stefano Luciano Ciurli
# [[Journal:JBIC:24|Solution structure and metal ion binding sites of the human CPEB3 ribozyme's P4 domain]], Miriam Skilandat, Magdalena Rowinska-Zyrek and Roland K. O. Sigel
# [[Journal:JBIC:25|Synthesis, characterization and binding properties towards CT-DNA and Lipoxygenase, of mixed ligand silver(I) complexes with 2-mercapto-thiazole and its derivatives and triphenylphosphine.]], L. Kyros, C.N. Banti, N. Kourkoumelis, M. Kubicki, I. Sainis and S.K. Hadjikakou
# [[Journal:JBIC:26|Fluoride inhibition of Sporosarcina pasteurii urease: structure and thermodynamics]], Stefano Benini, Michele Cianci, Luca Mazzei and Stefano Ciurli
# [[Journal:JBIC:27|Aromatic aldehydes at the active site of Aldehyde Oxidoreductase from Desulfovibrio gigas: Reactivity and Molecular Details of the Enzyme-Substrate and Enzyme-Product Interactions]], Correia HD, Marangon J, Brondino CD, Moura JJ, Romao MJ, Gonzalez PJ, Santos-Silva T
# [[Journal:JBIC:28|Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states]], Anne Volbeda, Lydie Martin, Elodie Barbier, Oscar Gutierrez-Sanz, Antonio L. De Lacey, Pierre-Pol Liebgott, Sebastien Dementin, Marc Rousset, Juan Fontecilla-Camps
# [[Journal:JBIC:29|High-resolution crystal structure of Z-DNA in complex with Cr3+ cations]], Pawel Drozdzal, Miroslaw Gilski, Ryszard Kierzek, Lechoslaw Lomozik, Mariusz Jaskolski
# [[Journal:JBIC:30|Structural Characterization of Metal Binding to a Cold-adapted Frataxin]], Martín E. Noguera, Ernesto A. Roman, Juan B. Rigal, Alexandra Cousido-Siah, André Mitschler, Alberto Podjarny, and Javier Santos
# [[Journal:JBIC:31|Conformational control of the binding of diatomic gases to cytochrome c’]], Andreea Manole, Demet Kekilli, Dimitri A. Svistunenko, Michael T. Wilson, Paul S. Dobbin, Michael A. Hough
# [[Journal:JBIC:32|Analyzing the Catalytic Role of Active Site Residues in the Fe-Type Nitrile Hydratase from ''Comamonas testosteroni'' Ni1]], Salette Martinez, Rui Wu, Karoline Krzywda, Veronika Opalka, Hei Chan, Dali Liu, and Richard C. Holz
# [[Journal:JBIC:33|Structural characterization of zinc-bound Zmp1, a zinc-dependent metalloprotease secreted by Clostridium difficile]], Jeffrey T. Rubino, Manuele Martinelli, Francesca Cantini, Andrea Castagnetti, Rosanna Leuzzi, Lucia Banci and Maria Scarselli
===JBSD ''Journal of Biomolecular Structure and Dynamics''===
# [[Journal:JBSD:1|An Insight to the Dynamics of Conserved Water Mediated Salt Bridge Interaction and Inter-Domain Recognition in hIMPDH Isoforms]], Hridoy R Bairagya and Bishnu P Mukhopadhyay
# [[Journal:JBSD:2|Elucidation by NMR solution of neurotensin in Small Unilamellar Vesicle environment: molecular surveys for neurotensin receptor recognition]], Grégory Da Costa, Arnaud Bondon, Olivier Delalande, Liza Mouret, Jean-Pierre Monti
# [[Journal:JBSD:3|Gating and conduction of nano-channel forming proteins, a computational approach]], A.B. Besya, H. Mobasheri, M.R. Ejtehadi
# [[Journal:JBSD:6|Evidence-based docking of the urease activation complex]], Rodrigo Ligabue-Braun, Rafael Real-Guerra, Célia Regina Carlini, Hugo Verli
# [[Journal:JBSD:5|Influence of divalent magnesium ion on DNA: molecular dynamics simulation studies]], Sanchita Mukherjee and Dhananjay Bhattacharyya
# [[Journal:JBSD:4|Dominant-negative Effects in Prion Diseases: Insights from Molecular Dynamics Simulations on Mouse Prion Protein Chimeras]], Xiaojing Cong, Salvatore Bongarzone, Gabriele Giachin, Giulia Rossetti, Paolo Carloni, Giuseppe Legname
# [[Journal:JBSD:7|Protein flexibility and conformational states of Leishmania antigen eIF-4A: Identification of a novel plausible protein adjuvant using comparative genomics and molecular modeling]], Ning-Ning Wei, Adel Hamza, Ce Hao, Trudy Johnson-Scalise, Zhilong Xiu, Frederick Naftolin, Chang-Guo Zhan
# [[Journal:JBSD:8|Docking and molecular dynamics studies of peptide inhibitors of ornithine decarboxylase: a rate-limiting enzyme for the metabolism of ''Fusarium solani'']], Sanchita, Rashi Chauhan, Garima Soni, Babu Sudhamalla, Ashok Sharma
# [[Journal:JBSD:9|Carbon monoxide binding to the heme group at the dimeric interface modulates structure and copper accessibility in the Cu,Zn superoxide dismutase from ''Haemophilus ducreyi'': in silico and in vitro evidences]], Giovanni Chillemi, Serena De Santis, Mattia Falconi, Giordano Mancini, Valentina Migliorati, Andrea Battistoni, Francesca Pacello, Alessandro Desideri, Paola D’Angelo
# [[Journal:JBSD:10|Para-(benzoyl)-phenylalanine as a potential inhibitor against LpxC of ''Leptospira spp.'': Homology modeling, docking and molecular dynamics study]], Dibyabhaba Pradhan, Vani Priyadarshini, Manne Munikumar, Sandeep Swargam, Amineni Umamaheswari & Aparna Bitla
# [[Journal:JBSD:11|Drug resistance mechanism of PncA in ''Mycobacterium Tuberculosis'']], Vidya Rajendran and Rao Sethumadhavan
# [[Journal:JBSD:12|Analysis of Delta–Notch interaction by molecular modeling and molecular dynamic simulation studies]], Riddhi Majumder, Sujata Roy, Ashoke Ranjan Thakur
# [[Journal:JBSD:13|Mechanism of BAG1 repair on Parkinson’s disease-linked DJ1 mutation]], Calvin Yu-Chian Chen
# [[Journal:JBSD:14|Traditional Chinese medicine as dual guardians against hypertension and cancer?]], Weng Ieong Tou, Calvin Yu-Chian Chen
# [[Journal:JBSD:15|The molecular origin of the MMR-dependent apoptosis pathway from dynamics analysis of MutSα-DNA complexes]], Lacramioara Negureanu, Freddie R. Salsbury
# [[Journal:JBSD:16|The extracellular subunit interface of the 5-HT3 receptors: a computational alanine scanning mutagenesis study]], Francesca De Rienzo, Arménio J. Moura Barbosa, Marta A.S. Perez, Pedro A. Fernandes, Maria J. Ramos, Maria Cristina Menziani
# [[Journal:JBSD:17|DNA Conformation and Energy in Nucleosome Core: A Theoretical Approach]], Davood Norouzi and Farshid Mohammad-Rafiee
# [[Journal:JBSD:18|Molecular modeling study for conformational changes of Sirtuin 2 due to substrate and inhibitor binding]], Sugunadevi Sakkiah, Meganathan Chandrasekaran, Yuno Lee, Songmi Kim, Keun Woo Lee
# [[Journal:JBSD:19|Crystal structure of the CN-hydrolase SA0302 from the pathogenic bacterium ''Staphylococcus aureus'' belonging to the Nit and NitFhit Branch of the nitrilase superfamily]], Roni D. Gordon, Wei Qiu, Vladimir Romanov, Kim Lam, Maria Soloveychik, Diana Benetteraj, Kevin P. Battaile, Yuri N. Chirgadze, Emil F. Pai, and Nickolay Y. Chirgadze
# [[Journal:JBSD:20|Insight into TPMT*23 Mutation Mis-folding Using Molecular Dynamics Simulation and Protein Structure Analysis]], Sofiene Larif, Chaker Ben Salem, Zohra Soua, Houssem Hmouda, Kamel Bouraoui
# [[Journal:JBSD:21|Identification of structural motifs in the E2 glycoprotein of Chikungunya involved in virus - host interaction]], J. Asnet Mary, R. Paramasivan, B.K. Tyagi, Surender Mohan and R. Shenbagarathai
# [[Journal:JBSD:22|Molecular dynamics simulations of the thermal stability of tteRBP and ecRBP]], Xian-li Feng, Xi Zhao, Hui Yu, Tie-dong Sun, Xu-ri Huang
# [[Journal:JBSD:23|Molecular Dynamics Simulation to Investigate the Impact of Disulfide Bond Formation on Conformational Stability of Chicken Cystatin I66Q Mutant]], Jianwei He, Linan Xu, Zhiyuan Zou, Nobuhiro Ueyama, Hui Li, Akio Kato, Gary W. Jones, Youtao Song
# [[Journal:JBSD:24|Insights into the drug resistance induced by the BaDHPS mutations: molecular dynamic simulations and MM/GBSA studies]], Wen-Ting Chu, Ji-Long Zhang, Qing-Chuan Zheng, Lin Chen, Qiao Xue, and Hong-Xing Zhang
# [[Journal:JBSD:25|Remarkable Disparity in Mechanical Response among the Extracellular Domains of Type I and II Cadherins]], Liu Ruchuan, Fei Wu and Jean Paul Thiery
# [[Journal:JBSD:26|Investigation on the Site-Selective Binding of Bovine Serum Albumin by Erlotinib Hydrochloride]], Yan Liu, Mingmao Chen, Zhipu Luo, Jingjing Lin, Ling Song
# [[Journal:JBSD:27|Interhelical loops within the bHLH domain are determinant in maintaining TWIST1-DNA complexes]], Charlotte Bouard, Raphael Terreux, Jennifer Hope, Julie Anne Chemelle, Alain Puisieux, Stéphane Ansieau, Lea Payen
# [[Journal:JBSD:28|Investigation of Silent Information Regulator 1 (Sirt1) Agonists from Traditional Chinese Medicine]], Kuan-Chung Chen, Yi-Ru Jian, Mao-Feng Sun, Tung-Ti Chang, Cheng-Chun Lee & Calvin Yu-Chian Chen
# [[Journal:JBSD:29|Han ethnicity-specific type 2 diabetic treatment from traditional Chinese medicine?]], Kuan-Chung Chen, Su-Sen Chang, Fuu-Jen Tsai, Calvin Yu-Chian Chen
# [[Journal:JBSD:30|Conformational dynamics of full-length inducible human Hsp70 derived from microsecond molecular dynamics simulations in explicit solvent]], Adrien Nicolaï, Patrice Delarue and Patrick Senet
# [[Journal:JBSD:31|Non-specificity and synergy at the binding site of the carboplatin-induced DNA adduct via molecular dynamics simulations of the MutSα-DNA recognition complex]], Lacramioara Negureanu & Freddie Salsbury, Jr
# [[Journal:JBSD:32|Cooperative Stabilization of Zn<sup>2+</sup>: DNA Complexes Through Netropsin Binding in the Minor Groove of FdU-Substituted DNA]], Supratim Ghosh, Freddie R. Salsbury Jr., David A. Horita and William H. Gmeiner
# [[Journal:JBSD:33|Probing the Structure of ''Mycobacterium tuberculosis'' MbtA: Model Validation Using Molecular Dynamics Simulations and Docking Studies]], Lakshmi Maganti, Open Source Drug Discovery Consortium & Nanda Ghoshal
# [[Journal:JBSD:34|Systematic investigation of predicted effect of nonsynonymous SNPs in human prion protein gene: A molecular modeling and molecular dynamics study]], Samad Jahandideha & Degui Zhia
# [[Journal:JBSD:35|A Possible Strategy against Head and Neck Cancer: ''In Silico''. Investigation of Three-in-One inhibitors]], Yung-An Tsou, Kuan-Chung Chen, Su-Sen Chang, Yeong-Ray Wen, Calvin Yu-Chian Chen
# [[Journal:JBSD:36|Structural Insights into the South African HIV-1 Subtype C Protease: Impact of hinge region dynamics and flap flexibility in drug resistance]], Previn Naicker, Ikechukwu Achilonu, Sylvia Fanucchi, Manuel Fernandes, Mahmoud A.A. Ibrahim, Heini W. Dirr, Mahmoud E.S. Soliman, and Yasien Sayed
# [[Journal:JBSD:37|Interaction of Piscidin-1 with Zwitterionic Versus Anionic Membranes: a Comparative Molecular Dynamics Study]], Arezoo Rahmanpour; Mohammad Mehdi Ghahremanpour; Faramarz Mehrnejad, Majid Erfani Moghaddam
# [[Journal:JBSD:38|Memory-Enhancement by Traditional Chinese Medicine?]], I-Chi Hung, Su-sen Chang, Pei-Chun, Chang, Cheng-Chun Lee, Calvin Yu-Chian Chen
# [[Journal:JBSD:39|The remarkable efficiency of a Pin-II proteinase inhibitor sans two conserved disulfide bonds is due to enhanced flexibility and hydrogen-bond density in the reactive loop]], Rakesh S. Joshi, Manasi Mishra, Vaijayanti A. Tamhane, Anirban Ghosh, Uddhavesh Sonavane, C. G. Suresh, Rajendra Joshi, Vidya S. Gupta and Ashok P. Giri
# [[Journal:JBSD:40|Traditional Chinese medicine application in HIV: An ''in silico'' study]], Hung-Jin Huanga, Yi-Ru Jianb, Calvin Yu-Chian Chen
# [[Journal:JBSD:41|Molecular Mechanism of HIV-1 gp120 Mutations That Reduce CD4 Binding Affinity]], Kristin Kassler and Heinrich Sticht
===JMB ''Journal of Molecular Biology''===
# [[Journal:JMB:1|Cyt1Aa Toxin: High Resolution Structure Reveals Implications for its Membrane-Perforating Function]], Cohen S, Albeck S, Ben-Dov E, Cahan R, Firer M, Zaritsky A, Dym O.
# [[Journal:JMB:2|Catalytic versatility and backups in enzyme active sites: The case of serum paraoxanase 1]], Moshe Ben-David, Mikael Elias, Jean-Jacques Filippi, Elisabet Dunach, Israel Silman, Joel Sussman and Dan Tawfik, PhD
# [[Journal:JMB:3|Catalytic metal ion rearrangements underline promiscuity and evolvability of a metalloenzyme]], Moshe Ben-David, Grzegorz Wieczorek, Mikael Elias, Israel Silman, Joel L. Sussman and Dan S. Tawfik
===JMedChem ''Journal of Medicinal Chemistry''===
# [[Journal:JMedChem:1|Structure of estradiol metal chelate and estrogen receptor complex: The basis for designing a new class of SERMs]], Min-Jun Li, Harry M. Greenblatt, Orly Dym, Shira Albeck, Adi Pais, Chidambaram Gunanathan, David Milstein, Hadassa Degani, and Joel L. Sussman
===JSB ''Journal of Structural Biology''===
# [[Journal:JSB:1|Structural and functional insights into a dodecameric molecular machine – The RuvBL1/RuvBL2 complex]], Sabine Gorynia, Tiago M. Bandeiras, Filipa G. Pinho, Colin E. McVey, Clemens Vonrhein, Adam Round, Dmitri I. Svergun, Peter Donner, Pedro M. Matias and Maria Arménia Carrondo
===MicroPubl Biol ''MicroPublication Biology''===
# [[Journal:MicroPubl Biol:000570|Biochemical and structural characterization of the flavodoxin-like domain of the ''Schizosaccharomyces japonicus'' putative tRNAPhe 4-demethylwyosine synthase TYW1 in complex with FMN]], Ljiljana Sjekloća, Adrian R. Ferré-D’Amaré
# [[Journal:MicroPubl Biol:000574|''Gossypium hirsutum'' gene of unknown function, Gohir.A02G044702.1, encodes a potential B3 Transcription Factor of the REM subfamily]], Michael Allen, Amanda M. Hulse-Kemp, Amanda R. Storm
# [[Journal:MicroPubl Biol:000606|The SSU Processome Component Utp25p is a Pseudohelicase]], Rafe Helwer and J. Michael Charette
# [[Journal:MicroPubl Biol:000670|''Gossypium hirsutum'' gene of unknown function, Gohir.A02G039501.1, encodes a potential DNA-binding ALOG protein involved in gene regulation]], Jonathan Zirkel, Amanda M. Hulse-Kemp, Amanda R. Storm
# [[Journal:MicroPubl Biol:000669|''Gossypium hirsutum'' gene Gohir.A03G007700.1 encodes a potential VAN3-binding protein with a phosphoinositide-binding site]], Emma R. Smith, Lauryn R. Caulley, Amanda M. Hulse-Kemp, Amanda R Storm, Angela K. Stoeckman
# [[Journal:MicroPubl Biol:000763|Quaternary structure analysis of IRE1]], Samirul Bashir, Debnath Pal, Ozaira Qadri, Mariam Banday, and Khalid Majid Fazili
# [[Journal:MicroPubl Biol:000867|''Gossypium hirsutum'' gene of unknown function Gohir.A03G0737001 encodes a potential Chaperone-like Protein of protochlorophyllide oxidoreductase (CPP1)]], Alana N. Osborne, Andrew Osagiede, Amanda R. Storm, Amanda M. Hulse-Kemp, Angela K. Stoeckman
# [[Journal:MicroPubl Biol:000868|''Gossypium hirsutum'' gene of unknown function Gohir.A02G131900 encodes a potential plant-specific, dual-domain exo-1,3-β-glucosidase]], Gillian Hernandez, Amanda M Hulse-Kemp, and Amanda R Storm
# [[Journal:MicroPubl Biol:001418|Human Structural Homologues of SARS-CoV-2 PLpro as Anti-Targets: A Strategic Panel Analysis]], Abdullah I. Al-Homoudi
# [[Journal:MicroPubl Biol:001838|Structural Basis for how Sialoglycan-binding Viridans Streptococci Accommodate Ligands that Exceed the Characterized Binding Site]], KeAndreya Morrison, Kole Martin, Hai Yu, Xi Chen, TM Iverson
===Molecular Cell ''''===
# [[Journal:Molecular Cell:1|Automated computational design of human enzymes for high bacterial expression and stability]], Adi Goldenzweig, Moshe Goldsmith, Shannon E Hill, Or Gertman, Paola Laurino, Yacov Ashani, Orly Dym, Tamar Unger, Shira Albeck, Jaime Prilusky, Raquel L Lieberman, Amir Aharoni, Israel Silman, Joel L Sussman, Dan S Tawfik and Sarel J Fleishman
# [[Journal:Molecular Cell:2|Automated design of efficient and functionally diverse enzyme repertoires]], Olga Khersonsky, Rosalie Lipsh, Ziv Avizemer, Yacov Ashani, Moshe Goldsmith, Haim Leader, Orly Dym, Shelly Rogotner, Devin L. Trudeau, Jaime Prilusky, Pep Amengual-Rigo, Victor Guallar, Dan S. Tawfik, and Sarel J. Fleishman
===Neuropharmacology ===
# [[Journal:Neuropharmacology:1|Slow-binding inhibitors of acetylcholinesterase of medical interest]], Sofya V. Lushchekina and Patrick Masson
# [[Journal:Neuropharmacology:2|Computational Studies on Cholinesterases: Strengthening our Understanding of the Integration of Structure, Dynamics and Function]], Joel L. Sussman and Israel Silman
===PLoS ONE ===
# [[Journal:PLoS ONE:1|Antiviral Activity of 3(2H)- and 6-Chloro-3(2H)-Isoflavenes against Highly Diverged, Neurovirulent Vaccine-Derived, Type2 Poliovirus Sewage Isolates]], Lester M. Shulman, Danit Sofer, Yossi Manor, Ella Mendelson, Jean Balanant, Anna Laura Salvati, Francis Delpeyroux, Lucia Fiore
# [[Journal:PLoS ONE:2|Structural Basis of Enzymatic Activity for the Ferulic Acid Decarboxylase (FADase) from Enterobacter sp. Px6-4]], Wen Gu, Jinkui Yang, Zhiyong Lou, Lianming Liang, Yuna Sun, Jingwen Huang, Xuemei Li, Yi Cao, Zhaohui Meng, Ke-Qin Zhang
===PMC ''Perspectives in Medicinal Chemistry''===
# [[Journal:PMC:1|Stereochemical Basis for a Unified Structure Activity Theory of Aromatic and Heterocyclic Rings in Selected Opioids and Opioid Peptides]], Joel S. Goldberg
===Protein Science ''''===
# [[Journal:Protein Science:1|Structural and functional characterization of the interaction of the photosensitizing probe methylene blue with ''Torpedo californica'' acetylcholinesterase]], Aviv Paz, Esther Roth, Yacov Ashani, Yechun Xu, Valery L. Shnyrov, Joel L. Sussman, Israel Silman, and Lev Weiner
# [[Journal:Protein Science:2|The Impact of Crystallization Conditions on Structure-Based Drug Design: a Case Study on the Methylene Blue/Acetylcholinesterase Complex]], Orly Dym, Wanling Song, Clifford Felder, Esther Roth, Valery Shnyrov, Yacov, Ashani, Yechun Xu, Robbie P. Joosten, Lev Weiner, Joel L. Sussman, and Israel Silman
# [[Journal:Protein Science:3|''Torpedo californica'' acetylcholinesterase is stabilized by binding of a divalent metal ion to a novel and versatile 4D motif]], Israel Silman, Valery L. Shnyrov, Yacov Ashani, Esther Roth, Anne Nicolas, Joel L Sussman, and Lev Weiner
# [[Journal:Protein Science:4|Why is binding of a divalent metal cation to a structural motif containing four carboxylate residues not accompanied by a conformational change?]], Lushchekina, Weiner, Ashani, Emrizal, Firdaus-Raih, Silman & Sussman
===Proteins ''''===
# [[Journal:Proteins:2|Protein Stability and ''in Vivo'' Concentration of Missense Mutations in Phenylalanine Hydroxylase]], Zhen Shi, Jenn Sellers, and John Moult
# [[Journal:Proteins:3|Do ‘''Newly Born''’ Orphan Proteins Resemble ‘''Never Born''’ Proteins? A Study Using Three Deep Learning Algorithms]], Jing Liu, Rongqing Yuan, Wei Shao, Jitong Wang, Israel Silman and Joel Sussman
===Science ===
# [[Journal:Science:1|Structural basis of transcription activation]], Yu Feng, Yu Zhang, Richard H. Ebright
===Structure ===
# [[Journal:Structure:1|Promiscuous Protein Binding as a Function of Protein Stability]], Ruth Cohen-Khait, Orly Dym, Shelly Hamer-Rogotner and Gideon Schreiber

Journal:Acta Cryst D:S2059798326002846

2026-10-03T10:22:38Z

Jaime Prilusky:

<StructureSection load='' size='450' side='right' scene='11/1121112/026_21ak_Cartoon_loop_pse/1' caption='Cryo-EM reconstruction of ArnA obtained from the dataset. Ab initio reconstruction produced a 3-fold-symmetric map corresponding to the ArnA hexamer at 3.23 Å (PDB-ID [[21ak]]). The density is consistent with previously reported ArnA architectures, confirming that the dominant particles in the dataset correspond to ArnA contaminant, rather than the intended target complex.'>
===Cryo-EM reveals ArnA contamination during puriﬁcation of a ciliary protein complex===
<big>Xuguang Jiang, Masahide Kikkawa</big> <ref>doi: 10.1107/S2059798326002846</ref>

<br><b>Molecular Tour</b><br>
'''Protein purification does not always yield what it seems'''. While determining the cryo-EM structure of a soluble KIF17-IFT70 ciliary protein complex, we found that a minor bacterial contaminant dominated the structural dataset. SDS-PAGE, size-exclusion chromatography and mass spectrometry supported the presence of the intended proteins and gave little warning of a major contaminant. Cryo-EM instead revealed ArnA.

'''Explore the structure''':
Render separately <scene name='11/1121112/026_both/9.spt'>21ak</scene>, (this study) and <scene name='11/1121112/026_both/2.spt '>9v5h</scene> (Caliseki et al.<ref name="Caliseki">PMID:40927951</ref>) or <scene name='11/1121112/026_both/3.spt '>compare both</scene> structures superimposed.
<p/>It is also interesting to
<jmol>
<jmolButton>
<script>
script /scripts/11/1121112/026_both/10.spt </script>
<text>animate between 21ak and 9v5h</text>
</jmolButton>
<jmolButton>
<script> animation Off </script>
<text>animation off </text>
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</jmol>.

[[Image:026 Fig 1ax.png|255px|right|thumb|'''Fig. 1.''' Biochemical QC was misleading: ArnA (~74 kDa) overlaps with KIF17 (~79 kDa) and IFT70 (~76 kDa) on SDS-PAGE. ArnA peptides were recognized only retrospectively; contrast adjustment also reveals a faint ~74 kDa band (right panel) consistent with ArnA.]]

<b>Why ArnA wins in cryo-EM</b>. ArnA forms a stable, highly symmetric hexamer that produces well-defined particle views and aligns efficiently during single-particle analysis. The intended KIF17-IFT70 complex was low-yield, flexible and prone to aggregation. Thus, even a small amount of ArnA could contribute a disproportionate number of high-quality particles and dominate the final reconstruction. The map and atomic model closely match previously determined ArnA structure<ref name="Caliseki"></ref>.

<b>Cryo-EM reveals what biochemical QC missed</b>. Micrographs contained aggregates together with dispersed, homogeneous particles, and 2D classification produced unusually clean threefold-symmetric views. Ab initio reconstruction identified the particles as the ArnA hexamer (Fig. 2); D3 refinement yielded a 3.23 Å reconstruction. No convincing KIF17-IFT70 classes were found. The close agreement with the previously reported ArnA structure made the contaminant unambiguous.

[[Image:026 Fig 2d.png|250px|left|thumb|'''Fig. 2.''' Comparison of cryo-EM maps. The map from this study closely matches ArnA reported by Caliseki et al.<ref name="Caliseki" />, showing that the dominant reconstruction is ArnA rather than the intended KIF17-IFT70 ciliary protein complex.]]

<b>Practical lesson</b>. Biochemical abundance and structural visibility are not equivalent. Rigid endogenous assemblies such as ArnA hexamers may remain inconspicuous during purification yet become immediately prominent by electron microscopy. Early negative-stain or cryo-EM screening, careful inspection of 2D classes, and awareness of recurrent host-derived contaminants can prevent substantial microscope time being spent on unintended targets.

<b>Take-home message for the I3DC</b>. ArnA (PDB 21AK; EMD-67448) is both an atomic structure and a methodological warning: in cryo-EM, structural “fitness” for particle alignment can matter more than biochemical abundance. The symmetry and rigidity that make ArnA an excellent cryo-EM specimen are also what make it a troublesome contaminant.

(PDB 21AK; EMD-67448)
<b>References</b>
<references/>
</StructureSection>
__NOEDITSECTION__

User:Masaki Unno

2026-10-03T03:34:55Z

Jaime Prilusky:

* Position: Professor
* Institution: Ibaraki University
* City: Hitachi
* State/Province: Ibaraki
* Country: Japan
* Field of Expertise or Study: Structural Biology
* ORCID ID: 0000-0002-4975-5696

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2026-10-02T04:50:32Z

Jaime Prilusky:

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Main Page

2026-10-01T16:17:04Z

Jaime Prilusky: Reverted edit by Jaime Prilusky (talk) to last revision by Angel Herraez

<table id="tableColumnsMainPage" >
<tr><td colspan='3' style="background:#F5F5FC; border:1px solid #ddd;">
<div id="issn">'''''ISSN 2310-6301'''''</div>
<div id="headerOne">As <b>life is more than 2D</b>, Proteopedia helps to bridge the gap between 3D structure and function of biomacromolecules.</div>
<div id="headerTwo"><b>Proteopedia</b> presents this information in a user-friendly way as a '''collaborative & free 3D-encyclopedia of proteins & other biomolecules.'''
</div>
</td>
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<tr id="mainPageSections"><th class="mainPageSectionA">Selected Research Pages</th>
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<tr id="rowFeatured"><td>{{Proteopedia:Featured SEL/{{#expr: {{#time:U}} mod {{Proteopedia:Number of SEL articles}}}}}}</td>
<td>{{Proteopedia:Featured JRN/{{#expr: {{#time:U}} mod {{Proteopedia:Number of JRN articles}}}}}}</td>
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Main Page

2026-10-01T16:16:43Z

Jaime Prilusky:

<table id="tableColumnsMainPage" >
<tr><td colspan='3' style="background:#F5F5FC; border:1px solid #ddd;">
<div id="issn">'''''ISSN 2310-6301'''''</div>
<div id="headerOne">As <b>life is more than 2D</b>, Proteopedia helps to bridge the gap between 3D structure and function of biomacromolecules.</div>
<div id="headerTwo"><b>Proteopedia</b> presents this information in a user-friendly way as a '''collaborative & free 3D-encyclopedia of proteins & other biomolecules.'''
</div>
</td>
</tr>
<tr id="mainPageSections"><th class="mainPageSectionA">Selected Research Pages</th>
<th class="mainPageSectionB">In Journals</th>
<th class="mainPageSectionC">Education</th>
</tr>
<tr id="rowFeatured">
<td colspan="3">
<div class="proteopedia-featured-row">
<div class="proteopedia-featured" data-featured-set="SEL"></div>
<div class="proteopedia-featured" data-featured-set="JRN"></div>
<div class="proteopedia-featured" data-featured-set="EDU"></div>
</div>
</td>
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<tr>
<td>[[Proteopedia:About|About]]</td>
<td>[[Special:Contact|Contact]]</td>
<td>[[Template:MainPageNews|Hot News]]</td>
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User talk:Xiaojing Song

2026-09-29T14:28:19Z

Jaime Prilusky: Welcome!

'''Welcome to ''Proteopedia''!''' We hope you will contribute much and well. You will probably want to watch the narrated [[Proteopedia:Video_Guide|video guide]] and use the [[Help:Contents|help pages]] for later reference. Again, welcome and have fun! . [[User:Jaime Prilusky|Jaime Prilusky]] ([[User talk:Jaime Prilusky|talk]]) 14:28, 29 September 2026 (UTC)

User:Xiaojing Song

2026-09-29T14:28:19Z

Jaime Prilusky: Creating user page for new user.

Position: Lecturer
Institution (NO ABBREVIATIONS): School of Basic Medicine, Nanchang Medical College
City: Nanchang
State/Province: Jiangxi
Country: China
Field of Expertise or Study: Structural and functional studies of membrane proteins

User:Jaime Prilusky/Test/Simple

2026-09-22T20:03:57Z

Jaime Prilusky:

<StructureSection load='' size='340' side='right' caption='Caption for this structure' scene=''>

<jmol>
<jmolButton>
<text>21ak</text>
<script>
script /wiki/scripts/11/1121112/026_both/1.spt;
animation MODE LOOP; animation on;
</script>
</jmolButton>
</jmol>

<scene name='10/1089011/Traditional/1'>traditional</scene>

<scene name='10/1089011/3recS1/1'>3recS1</scene>

This scene was saved as <scene name='11/1112693/Next/14'>PNGJ</scene>

Created by loading Camp.pse, and adding isosurface and colors.
Movement, quality and caption are Ok.
Missing color reference.

A heavy structure with <scene name='11/1112693/Next/15'>surfaces</scene>

Started from Figure_2B.pse, adding colors, movement and label.


</StructureSection>
== References ==
<references/>

Journal:Acta Cryst D:S2059798326002846

2026-09-22T20:00:01Z

Jaime Prilusky:

<StructureSection load='' size='450' side='right' scene='11/1121112/026_21ak_Cartoon_loop_pse/1' caption='Cryo-EM reconstruction of ArnA obtained from the dataset. Ab initio reconstruction and subsequent refinement produced a threefold-symmetric map corresponding to the ArnA hexamer, refined to an overall resolution of 3.23 Å (PDB-ID [[21ak]]). The density is consistent with previously reported ArnA architectures, confirming that the dominant particles in the dataset correspond to ArnA contaminant, rather than the intended target complex.'>
===Cryo-EM reveals ArnA contamination during puriﬁcation of a ciliary protein complex===
<big>Xuguang Jiang, Masahide Kikkawa</big> <ref>doi: 10.1107/S2059798326002846</ref>

<br><b>Molecular Tour</b><br>
Protein purification does not always yield what it seems. While attempting to determine the cryo-EM structure of a soluble KIF17–IFT70 ciliary protein complex, we encountered a striking example of how a minor bacterial contaminant can dominate a structural dataset. Standard biochemical quality-control methods, including SDS–PAGE, size-exclusion chromatography and mass spectrometry, suggested that the intended proteins were present and provided little indication of a major contaminant. Cryo-EM, however, rather than the intended target (Fig. 1).

[[Image:026 Fig 1ax.png|400px|right|thumb|'''Fig. 1.''' The hidden contaminant. Conventional biochemical QC was misleading: ArnA (~74 kDa) overlaps closely with KIF17 (~79 kDa) and IFT70 (~76 kDa) on SDS–PAGE. ArnA peptides were not initially considered in data interpretation but were detected retrospectively upon reanalysis of the dataset. Upon contrast adjustment, an additional faint band migrating near 74 kDa can be discerned, consistent with the expected MW of ArnA, right panel in. This provides an effective visual introduction to the central problem.]]

The structure helps explain why ArnA can become such a troublesome contaminant in cryo-EM. ArnA forms a stable and highly symmetric hexamer, giving rise to well-defined particle views that align efficiently during single-particle analysis. In contrast, the intended KIF17–IFT70 complex was low-yield, flexible and prone to aggregation. Consequently, even a relatively small amount of ArnA could disproportionately contribute high-quality particles and dominate the final reconstruction. The resulting cryo-EM map and atomic model closely agree with previously determined ArnA structures, allowing the unexpected particles to be unambiguously identified.<br>

<b>Cryo-EM reveals what biochemical QC missed</b><br>
Cryo-EM immediately changed the interpretation of the sample. Micrographs contained aggregates along with dispersed, homogeneous particles, and 2D classification produced unusually clean, threefold-symmetric views. ''Ab initio'' reconstruction identified <scene name='11/1121112/027_21ak/1'>these particles</scene> as the <scene name='11/1121112/026_9v5h_aligned_on_21ak/1'>ArnA hexamer</scene>; refinement with D3 symmetry produced the final 3.23 Å reconstruction. No convincing classes corresponding to KIF17–IFT70 were found. The previously determined structure of Arna, looks virtually identical. <scene name='11/1121112/026_both/1'>21ak</scene> <scene name='11/1121112/026_both/2'>9v5h</scene> <scene name='11/1121112/026_both/3'>both</scene> <scene name='11/1121112/026_both/7'>animate</scene>.
<jmol>
<jmolButton>
<text>21ak</text>
<script>script /wiki/scripts/11/1121112/026_both/1.spt; animation MODE LOOP; animation on;</script>
</jmolButton>
</jmol>

[[Image:026 Fig 2d.png|400px|left|thumb|'''Fig. 2.''' Comparison cryo-EM maps of this study versus that of ArnA reported by Caliseki[<ref>PMID: 40927951</ref>.]] It is clear that what is seen is the contaminant in this study, ''i.e.'', Arna, and '''not''' the intended target complex, ''i.e.'', KIF17–IFT70 ciliary protein.

This case illustrates an important practical lesson for structural biology: biochemical abundance and structural visibility are not necessarily equivalent. Rigid endogenous assemblies, '''like the ArnA hexamers''', may remain inconspicuous during conventional purification and quality control yet become immediately apparent by electron microscopy. Early negative-stain or cryo-EM screening, careful inspection of 2D classes, and awareness of recurrent host-derived contaminants can therefore help prevent substantial investment of microscope time in unintended targets.<br>

<br><b>Take-home message for the I3DC</b>
<br>
ArnA (PDB 21AK; EMD-67448) is both an atomic structure and a methodological warning: in cryo-EM, structural “fitness” for particle alignment can matter more than biochemical abundance. The elegant symmetry and rigidity that make ArnA an excellent cryo-EM specimen are precisely what make it a dangerous contaminant.<br>

<b>References</b>
<references/>
</StructureSection>
__NOEDITSECTION__

User:Jaime Prilusky/Test/next

2026-09-22T14:08:15Z

Jaime Prilusky:

<StructureSection load='' size='400' side='right' caption='' scene=''>

1crn <scene name='11/1112693/1crn/2'>one</scene> <scene name='11/1112693/1crn/4'>two</scene>

* <scene name='11/1112693/Camp/3'>camp.pse 16.4.17</scene>
* <scene name='11/1112693/Camp/4'>camp.pse 16.4.15</scene>
* <scene name='11/1112693/Camp/5'>camp.pse 16.4.11</scene>
* <scene name='11/1112693/1hek/1'>1hek 16.4.11</scene>

# page Sandbox_JLS_09 - scene SB_JLS_09 #7
#+ <scene name='11/1112693/SB_JLS_09/2'>removed dots</scene>
#+ <scene name='11/1112693/SB_JLS_09/3'>removed dots + zoom-in</scene>
#+ <scene name='11/1112693/SB_JLS_09/4'>zoom-in</scene>
#+l<scene name='11/1112693/SB_JLS_09/5'>oad+save, no change</scene>
<br>---------------------------------------------------

# <scene name='11/1112693/3rec_surface/1'>3rec half surface</scene>
# + <scene name='11/1112693/3rec_surface/2'>zoom-in</scene>
# + <scene name='11/1112693/3rec_surface/3'>mesh-ribbon</scene>
---------------------------------------------------

<scene name='11/1112693/3rec/39'>simple 3rec</scene>

<scene name='11/1112693/Next/16'>3rec + surface</scene>

<scene name='11/1112693/Next/18'>Camp.pse</scene>

<scene name='11/1112693/3rec/38'>3rec smooth</scene>

<scene name='11/1112693/Next/21'>should not render</scene>

<scene name='11/1112693/3recs1/3'>3recs1 modified</scene>

<scene name='11/1112693/Acherock/2'>AChErock.pse</scene>

<scene name='11/1112693/Four_surfaces/1'>4 surfaces</scene>
<scene name='11/1112693/Four_surfaces/2'>four surfaces MEP colored</scene>

<scene name='10/1089011/Ktcylinders/1'>cylinders</scene>

<scene name='11/1112693/1cjg_11_models/8'>smooth transition</scene>

<scene name='11/1112693/1wtn/2'>1wtn</scene>

<scene name='11/1112693/1crn/1'>1crn</scene>

__NOTOC__
</StructureSection>
== References ==
<references/>

Journal:Acta Cryst F:S2053230X26009052

2026-09-19T09:10:58Z

Jaime Prilusky:

<StructureSection load='' size='450' side='right' scene='11/1121096/025_Initl_View_pse/4' caption='Cartoon representation of the mJuniper structure exhibiting the characteristic 11-stranded beta-barrel fold, like sfGFP, with the central chromophore-containing alpha-helix (PDB-ID [[29zn]]).'>
===Serendipitous crystal structure of mJuniper, a rationally designed cyan fluorescent protein===
<big>Alpay Aydin, Nathan Fraikin, Priscillia Lagoutte, Christian Lesterlin, Laurent Terradot</big> <ref>doi: 10.1107/S2053230X26009052</ref>
<hr/>
<b>Molecular Tour</b><br>
mJuniper is a monomeric cyan fluorescent protein (CFP) optimized for bacterial imaging, notable for having the fastest maturation kinetics ever recorded for a CFP. Originally used to improve the solubility of a target protein, its <scene name='11/1121096/025_new_map_x_pse/2'>high-resolution X-ray structure</scene> was serendipitously determined during an attempt to characterize a component of Helicobacter pylori type IV secretion system. The structure reveals a classic β-barrel scaffold and a chromophore with two rotameric states, arising from <scene name='11/1121096/025_pos_neg_mesh_pse/5'>specific radiation damage</scene> in its immediate environment.<br>
<b>References</b><br>
<references/>
</StructureSection>
__NOEDITSECTION__

Journal:Acta Cryst D:S2059798326002846

2026-09-16T05:35:27Z

Jaime Prilusky:

<StructureSection load='' size='450' side='right' scene='underdevelopment' caption=''>
===Cryo-EM reveals ArnA contamination during puriﬁcation of a ciliary protein complex===
<big>Xuguang Jiang, Masahide Kikkawa</big> <ref>doi: 10.1107/S2059798326002846</ref>
<hr/>
<b>Molecular Tour</b><br>
Protein purification does not always yield what it seems. While attempting to determine the cryo-EM structure of a soluble KIF17–IFT70 ciliary protein complex, we encountered a striking example of how a minor bacterial contaminant can dominate a structural dataset. Standard biochemical quality-control methods, including SDS–PAGE, size-exclusion chromatography and mass spectrometry, suggested that the intended proteins were present and provided little indication of a major contaminant. Cryo-EM, however, told a very different story: highly homogeneous, threefold-symmetric particles emerged during 2D classification, ultimately yielding a 3.23 Å reconstruction of the Escherichia coli protein ArnA rather than the intended KIF17–IFT70 complex.

The structure helps explain why ArnA can become such a troublesome contaminant in cryo-EM. ArnA forms a stable and highly symmetric hexamer, giving rise to well-defined particle views that align efficiently during single-particle analysis. In contrast, the intended KIF17–IFT70 complex was low-yield, flexible and prone to aggregation. Consequently, even a relatively small amount of ArnA could disproportionately contribute high-quality particles and dominate the final reconstruction. The resulting cryo-EM map and atomic model closely agree with previously determined ArnA structures, allowing the unexpected particles to be unambiguously identified.

This case illustrates an important practical lesson for structural biology: biochemical abundance and structural visibility are not necessarily equivalent. Rigid endogenous assemblies may remain inconspicuous during conventional purification and quality control yet become immediately apparent by electron microscopy. Early negative-stain or cryo-EM screening, careful inspection of 2D classes, and awareness of recurrent host-derived contaminants can therefore help prevent substantial investment of microscope time in unintended targets.
<b>References</b><br>
<references/>
</StructureSection>
__NOEDITSECTION__

Journal:Acta Cryst D:S2059798326002846

2026-09-16T05:35:00Z

Jaime Prilusky:

<StructureSection load='' size='450' side='right' scene='underdevelopment' caption=''>
===electronic reprint ISSN: 2059-7983 journals.iucr.org/d Cryo-EM reveals ArnA contamination during puriﬁcation of a ciliary protein complex===
<big>Xuguang Jiang, Masahide Kikkawa</big> <ref>doi: 10.1107/S2059798326002846</ref>
<hr/>
<b>Molecular Tour</b><br>
Protein purification does not always yield what it seems. While attempting to determine the cryo-EM structure of a soluble KIF17–IFT70 ciliary protein complex, we encountered a striking example of how a minor bacterial contaminant can dominate a structural dataset. Standard biochemical quality-control methods, including SDS–PAGE, size-exclusion chromatography and mass spectrometry, suggested that the intended proteins were present and provided little indication of a major contaminant. Cryo-EM, however, told a very different story: highly homogeneous, threefold-symmetric particles emerged during 2D classification, ultimately yielding a 3.23 Å reconstruction of the Escherichia coli protein ArnA rather than the intended KIF17–IFT70 complex.

The structure helps explain why ArnA can become such a troublesome contaminant in cryo-EM. ArnA forms a stable and highly symmetric hexamer, giving rise to well-defined particle views that align efficiently during single-particle analysis. In contrast, the intended KIF17–IFT70 complex was low-yield, flexible and prone to aggregation. Consequently, even a relatively small amount of ArnA could disproportionately contribute high-quality particles and dominate the final reconstruction. The resulting cryo-EM map and atomic model closely agree with previously determined ArnA structures, allowing the unexpected particles to be unambiguously identified.

This case illustrates an important practical lesson for structural biology: biochemical abundance and structural visibility are not necessarily equivalent. Rigid endogenous assemblies may remain inconspicuous during conventional purification and quality control yet become immediately apparent by electron microscopy. Early negative-stain or cryo-EM screening, careful inspection of 2D classes, and awareness of recurrent host-derived contaminants can therefore help prevent substantial investment of microscope time in unintended targets.
<b>References</b><br>
<references/>
</StructureSection>
__NOEDITSECTION__

Journal:Acta Cryst D:S2059798326002846

2026-09-16T05:34:02Z

Jaime Prilusky: Created page with "-"

User:Jaime Prilusky/Test/Simple

2026-09-15T18:10:08Z

Jaime Prilusky:

<StructureSection load='' size='340' side='right' caption='Caption for this structure' scene=''>

<scene name='11/1121095/q-deform/1'>q-deform</scene>

<scene name='10/1089011/Traditional/1'>traditional</scene>

<scene name='10/1089011/3recS1/1'>3recS1</scene>

This scene was saved as <scene name='11/1112693/Next/14'>PNGJ</scene>

Created by loading Camp.pse, and adding isosurface and colors.
Movement, quality and caption are Ok.
Missing color reference.

A heavy structure with <scene name='11/1112693/Next/15'>surfaces</scene>

Started from Figure_2B.pse, adding colors, movement and label.


</StructureSection>
== References ==
<references/>

Journal:Acta Cryst D:S2059798326000422

2026-09-15T09:57:48Z

Jaime Prilusky:

<StructureSection load='' size='450' side='right' scene='underdevelopment' caption=''>
===Crystal structure of Schistosoma mansoni cathepsin D1 in complex with a nanobody reveals the conformation of the propeptide-bound state===
<big>Kelly L. Parker, John D. Clarke, Xiaojiao Liu, Barbara F. Gomes, Lauren E.-A. Eyssen, Nicholas Furnham, Floriano Paes Silva-Jr, Raymond J. Owens</big> <ref>doi: 10.1107/S2059798326000422</ref>
<hr/>
<b>Molecular Tour</b><br>
Schistomiasis, also known as Bilhazia, is a tropical disease caused by parasitic worms and transmitted by freshwater snails. In a complex life cycle that involves a blood borne stage, the Schistosome worm produces proteases that digest haemaglobin, providing the amino acids that are essential for survival of the parasite. One of these digestive enzymes found in the gut of the parasite is the aspartyl protease, CathepsinD1 and given its key role in the life cycle of the schistosome worms is a potential drug target for treating Schistomiasis. Like other aspartyl proteases, Schistosome Cathepsin D1 is produced as an inactive pro-enzyme or zymogen so that it can be stored by the worm and only becomes catalytically active on exposure to the acidic pH in the gut of the parasite. Activation involves cleavage of a specific peptide sequence at the amino terminus of the enzyme which in turn exposes the active site.
We have determined the first crystal structure of Cathepsin D1 zymogen from the parasite, Schistosoma mansoni (abbreviated as SmCD1) revealing the conformation of the inactive enzyme. By immunising a llama with purified SmCD1, we produced a single domain antibody (nanobody) that bound with high affinity to the enzyme and determined the structure of the enzyme in complex with the nanobody. Comparison of SmCD1 to human Cathepsin D (hCD) and human Cathepsin E (hCE) shows that their structures are largely conserved, with the active site residues positioned in equivalent locations. Despite this structural similarity, the anti-SmCD1 nanobody did not bind to the human homologues, recognising a sequence that is conserved in schistosome parasites but not the human enzymes. Therefore, the nanobody provides a schistosome-specific tool and identifies a binding epitope on the enzyme for future structure-guided drug design of novel therapeutics for schistosomiasis.
<b>References</b><br>
<references/>
</StructureSection>
__NOEDITSECTION__

Journal:Acta Cryst D:S2059798326000422

2026-09-15T09:57:09Z

Jaime Prilusky:

<StructureSection load='' size='450' side='right' scene='underdevelopment' caption=''>
===Crystal structure of Schistosoma mansoni cathepsin D1 in complex with a nanobody reveals the conformation of the propeptide-bound state===
<big>Kelly L. Parker, John D. Clarke, Xiaojiao Liu, Barbara F. Gomes, Lauren E.-A. Eyssen, Nicholas Furnham, Floriano Paes Silva-Jr, Raymond J. Owensa, Professor Raymond J Owens</big> <ref>doi: 10.1107/S2059798326000422</ref>
<hr/>
<b>Molecular Tour</b><br>
Schistomiasis, also known as Bilhazia, is a tropical disease caused by parasitic worms and transmitted by freshwater snails. In a complex life cycle that involves a blood borne stage, the Schistosome worm produces proteases that digest haemaglobin, providing the amino acids that are essential for survival of the parasite. One of these digestive enzymes found in the gut of the parasite is the aspartyl protease, CathepsinD1 and given its key role in the life cycle of the schistosome worms is a potential drug target for treating Schistomiasis. Like other aspartyl proteases, Schistosome Cathepsin D1 is produced as an inactive pro-enzyme or zymogen so that it can be stored by the worm and only becomes catalytically active on exposure to the acidic pH in the gut of the parasite. Activation involves cleavage of a specific peptide sequence at the amino terminus of the enzyme which in turn exposes the active site.
We have determined the first crystal structure of Cathepsin D1 zymogen from the parasite, Schistosoma mansoni (abbreviated as SmCD1) revealing the conformation of the inactive enzyme. By immunising a llama with purified SmCD1, we produced a single domain antibody (nanobody) that bound with high affinity to the enzyme and determined the structure of the enzyme in complex with the nanobody. Comparison of SmCD1 to human Cathepsin D (hCD) and human Cathepsin E (hCE) shows that their structures are largely conserved, with the active site residues positioned in equivalent locations. Despite this structural similarity, the anti-SmCD1 nanobody did not bind to the human homologues, recognising a sequence that is conserved in schistosome parasites but not the human enzymes. Therefore, the nanobody provides a schistosome-specific tool and identifies a binding epitope on the enzyme for future structure-guided drug design of novel therapeutics for schistosomiasis.
<b>References</b><br>
<references/>
</StructureSection>
__NOEDITSECTION__

Pyruvate kinase 3D structures

2026-09-14T13:43:21Z

Jaime Prilusky:

==3D structures of pyruvate kinase==

Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|

*Pyruvate kinase muscle

**[[1t5a]], [[1zjh]], [[3bjf]], [[3bjt]], [[9hib]] - hPyK M2 muscle - human
**[[3g2g]], [[4qg6]], [[4qg8]], [[4qg9]], [[4qgc]], [[4wj8]], [[4yj5]], [[6b6u]], [[8hgf]] - hPyK M2 muscle (mutant)
**[[3srf]], [[3srh]] – hPyK M1 muscle
**[[6wp3]], [[6wp4]], [[6wp5]], [[6wp6]] – hPyK M2 muscle (mutant)
**[[1pkm]], [[1pyk]] – PyK muscle – cat
**[[1f3w]], [[8f5t]] – rPyK muscle – rabbit
**[[1f3x]], [[7r6y]] - rPyK muscle (mutant)

*Pyruvate kinase muscle binary complexes

**[[4b2d]], [[9hic]] - hPyK M2 muscle + fructose bisphosphate
**[[4rpp]] - hPyK M2 muscle (mutant) + fructose bisphosphate
**[[4fxj]] - hPyK M2 muscle + phenylalanine
**[[6gg3]] - hPyK M2 muscle + alanine
**[[6gg4]] - hPyK M2 muscle + phenylalanine
**[[6gg5]] - hPyK M2 muscle + tryptophan
**[[6gg6]] - hPyK M2 muscle + serine
**[[6nub]] - hPyK M2 muscle (mutant) + serine
**[[6nu1]] - hPyK M2 muscle + cysteine
**[[6nu5]] - hPyK M2 muscle (mutant) + cysteine
**[[6ttf]], [[6tti]], [[6ttq]] - hPyK M2 muscle + inhibitor – Cryo EM
**[[6tth]] - hPyK M2 muscle + threonine – Cryo EM
**[[6v74]], [[6v75]] - hPyK M2 muscle + asparagine
**[[6v76]] - hPyK M2 muscle + valine
**[[8g2e]], [[9iqq]], [[9o3b]] - hPyK M2 muscle + activator
**[[8f5u]] - rPyK muscle + pyruvate

*Pyruvate kinase muscle higher complexes

**[[3me3]] – hPyK M1/M2 muscle + aniline derivative + fructose bisphosphate
**[[4g1n]] - hPyK M1/M2 muscle + pyridazine derivative + oxalate
**[[3h6o]] - hPyK M1/M2 muscle + pyridazine derivative + fructose bisphosphate
**[[3gqy]], [[3gr4]], [[3u2z]] - hPyK M1/M2 muscle + piperazine derivative + fructose bisphosphate
**[[8hmq]], [[8hmr]], [[8hms]], [[8hmu]] - hPyK muscle (mutant) + Pi + fructose bisphosphate
**[[5x0i]] - hPyK M2 muscle (mutant) + serine + fructose bisphosphate
**[[7l21]] - hPyK M2 muscle (mutant) + oxalate + fructose bisphosphate
**[[6jfb]] - hPyK M2 muscle + serine + phosphate
**[[5x1v]], [[5x1w]] - hPyK M2 muscle + activator + fructose bisphosphate
**[[4jpg]] - hPyK M1/M2 muscle + pyrimidine derivative +fructosebisphosphate
**[[3srd]] - hPyK M1/M2 muscle + oxalate + fructose bisphosphate
**[[4fxf]] - hPyK M1/M2 muscle + oxalate + ATP + fructose bisphosphate
**[[3n25]] – rPyK M1/M2 muscle + proline + Mn + pyruvate
**[[2g50]] - rPyK M1/M2 muscle + alanine + Mn + pyruvate
**[[8f6m]] - rPyK muscle + Ala + Mn + ADP
**[[1pkn]] - rPyK muscle + Mn + pyruvate
**[[1aqf]] – rPyK muscle + Mg + phospholactate
**[[1a49]], [[1a5u]] - rPyK muscle + ATP + oxalate

*Pyruvate kinase liver

**[[9vxp]] - hPyK liver – Cryo EM
**[[2vgb]] – hPyK liver
**[[2vgf]], [[2vgg]], [[2vgi]] [[6nn5]], [[6nn7]], [[6nn8]], [[7qdn]] – hPyK liver (mutant)
**[[9w4q]], [[9w7y]], [[9w81]] - hPyK liver + activator – Cryo EM
**[[8tbs]], [[8tbt]], [[8tbu]] - hPyK liver + activator
**[[7fs7]] - hPyK liver + modulator
**[[9wdo]], [[9wdq]], [[9wdr]], [[9edt]] - hPyK liver + drug – Cryo EM
**[[8xfd]] - hPyK liver + activator
**[[9r3h]], [[9r3i]], [[9r3l]], [[9r3m]], [[9r3o]], [[9rdf]], [[9rfq]], [[9rft]] - hPyK liver + fluorescent probe
**[[9wez]] - hPyK liver + fructose bisphosphate – Cryo EM
**[[6nn4]] - hPyK M2 liver (mutant) + fructose bisphosphate
**[[6ech]], [[6eck]] - PyK liver + fructose bisphosphate - rat
**[[5sc8]], [[5sc9]], [[5sca]], [[5scb]], [[5scc]], [[5scd]], [[5sce]], [[5scf]], [[5scg]], [[5sch]], [[5sci]], [[5scj]], [[5sck]], [[5scl]], [[5sdt]], [[7qzu]] - hPyK liver + anthracene derivative + fructose bisphosphate
**[[7frv]], [[7frw]], [[7frx]], [[7fry]], [[7frz]], [[7fs0]], [[7fs1]], [[7fs2]], [[7fs3]], [[7fs4]], [[7fs5]], [[7fs6]], [[7fs8]], [[7fs9]], [[7fsa]], [[7fsb]], [[7fsc]], [[7fsd]] - hPyK liver + modulator + fructose bisphosphate
**[[4ima]], [[4ip7]] - hPyK liver (mutant) + citrate + adenosine + fructose bisphosphate

*Pyruvate kinase

**[[6du6]] – PyK - mosquito
**[[1pky]], [[4yng]], [[6k0k]] – EcPyK - Eschericia coli
**[[1e0t]], [[1e0u]], [[8edq]], [[8edr]], [[8eds]], [[8edt]], [[8eq0]], [[8eq1]], [[8eq3]], [[8eu4]] - EcPyK (mutant)
**[[3t05]], [[3t0t]] – SaPyK – Staphylococcus aureus
**[[3qtg]] – PyK – Pyrobaculum aerophilum
**[[4krz]] – TcPyK – Trypanosoma cruzei
**[[5wrp]] - MtPyK – Mycobacterium tuberculosis
**[[1pkl]], [[3e0w]], [[3hqn]] – LmPyK – Leishmania mexicana
**[[3khd]], [[7z4m]] – PfPyK – Plasmodium falciparum
**[[7z4q]], [[7z4r]] - PfPyK (mutant)
**[[3eoe]], [[3gg8]] – PyK – Toxoplasma gondii
**[[3ma8]], [[4drs]] – CpPyK – Cryptosporidium parvum
**[[2e28]] - PyK (mutant) – Geobacillus stearothermophilus
**[[7oo1]] – PaPyK – Pseudomonas aeruginosa
**[[7ueh]] – PyK – Zymomonas mobilis
**[[8ias]] - SpPyK – Streptococcus pneumoniae
**[[8iw2]] - PyK – Entamoeba histolytica

*Pyruvate kinase binary complex

**[[8x4r]] – hPyK + Phe
**[[3qv9]] – TcPyK + Ponceau S
**[[3qv6]] – LmPyK + acid blue 80
**[[3e0v]] – LmPyK + sulfate
**[[3hqq]] - LmPyK + fructose bisphosphate
**[[3qv8]] – LmPyK + benzothiazole
**[[3pp7]] – LmPyK + suramin
**[[3is4]], [[3ktx]] – LmPyK + pyrenetetrasulfonic acid
**[[3t07]] – SaPyK + bis-indole alkaloid
**[[4hyw]] – TbPyK + fructose bisphosphate – Trypanosoma brucei
**[[6su1]], [[6su2]] – PyK + citrate – Trypanosoma congolense
**[[5ws8]] - MtPyK + oxalate
**[[6p0y]] - CpPyK + ADP
**[[8iav]] - SpPyK + fructose bisphosphate
**[[8iat]] - SpPyK + oxalate
**[[8iaw]] - SpPyK + phosphoenolpyruvate
**[[7z4n]] -PfPyK + pyruvate
**[[8rtf]], [[8rvr]] -PyK + antibody – Trypanosoma congolense

*Pyruvate kinase higher complexes

**[[8xfd]] – hPyK + activator + fructose bisphosphate
**[[1a3w]] – yPyK + Mn + phosphoglycolic acid + fructose bisphosphate – yeast
**[[1a3x]] - yPyK + Mn + phosphoglycolic acid
**[[4hyv]] – TbPyK + phosphoenolpyruvate + fructose bisphosphate
**[[4kct]] – TbPyK + pyruvate + fructose bisphosphate
**[[4kcu]] – TbPyK + malate + fructose bisphosphate
**[[4kcv]] – TbPyK + oxoglutarate + fructose bisphosphate
**[[4kcw]] – TbPyK + oxalate + fructose bisphosphate
**[[4ks0]] – TcPyK + oxalate + fructose bisphosphate
**[[5ws9]] – MtPyK + oxalate + AMP + ATP
**[[5wsa]] – MtPyK + oxalate + glucose-6-phosphate
**[[5wsb]], [[5wsc]] – MtPyK + oxalate + glucose-6-phosphate + AMP
**[[6ito]] – MtPyK + oxalate + ribose-5-phosphate + AMP
**[[3hqo]] – LmPyK + ATP + oxalate
**[[3hqp]] - LmPyK + ATP + oxalate + fructose bisphosphate
**[[3qv7]] – LmPyK + acid blue 25 + Ponceau S
**[[3srk]] – LmPyK + saccharine + inhibitor
**[[6qxl]] – PaPyK + malonate + glucose-6-phosphate + Mg
**[[6ksh]] – PfPyK + oxalate + ATP
**[[8iax]] - SpPyK + fructose bisphosphate + phosphoenolpyruvate
**[[8iau]] - SpPyK + fructose bisphosphate + oxalate
**[[8xw6]], [[8xw7]], [[8xw8]], [[8xw9]], [[8zly]] - SpPyK + fructose bisphosphate + oxalate + nucleotide
}}

[[Category: Topic Page]]

Journal:Acta Cryst F:S2053230X26009052

2026-09-11T08:07:15Z

Jaime Prilusky:

<StructureSection load='' size='450' side='right' scene='underdevelopment' caption=''>
===Serendipitous crystal structure of mJuniper, a rationally designed cyan fluorescent protein===
<big>Alpay Aydin, Nathan Fraikin, Priscillia Lagoutte, Christian Lesterlin, Laurent Terradot</big> <ref>doi: 10.1107/S2053230X26009052</ref>
<hr/>
<b>Molecular Tour</b><br>
mJuniper is a monomeric cyan fluorescent protein (CFP) optimized for bacterial imaging, notable for having the fastest maturation kinetics ever recorded for a CFP. Originally used to improve the solubility of a target protein, its high-resolution X-ray structure was serendipitously determined during an attempt to characterize a component of Helicobacter pylori type IV secretion system. The structure reveals a classic β-barrel scaffold and a chromophore with two rotameric states, arising from specific radiation damage in its immediate environment.

<b>References</b><br>
<references/>
</StructureSection>
__NOEDITSECTION__

Journal:Acta Cryst F:S2053230X26009052

2026-09-10T15:08:49Z

Jaime Prilusky:

<StructureSection load='' size='450' side='right' scene='underdevelopment' caption=''>
===Crystal structure of mJuniper: a rationally designed cyan fluorescent protein===
<big>Dr Laurent Terradot</big> <ref>doi: 10.1107/S2053230X26009052</ref>
<hr/>
<b>Molecular Tour</b><br>

<b>References</b><br>
<references/>
</StructureSection>
__NOEDITSECTION__

Journal:Acta Cryst F:S2053230X26009052

2026-09-10T15:08:35Z

Jaime Prilusky: Created page with "-"

User talk:Ambar R. Gonzalez Mendieta

2026-09-09T17:19:15Z

Jaime Prilusky: Welcome!

User:Ambar R. Gonzalez Mendieta

2026-09-09T17:19:15Z

Jaime Prilusky: Creating user page for new user.

Position: Student
Institution (NO ABBREVIATIONS): Universidad del Valle de México
City: Iztacalco
State/Province: Ciudad de México
Country: México
Field of Expertise or Study: Medicine and sociology
ORCID ID: ---