21dt: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 21dt is ~~ON HOLD until Paper~~ Publication

==X-ray structure of the Haloalkane dehalogenase HaloTag7 labeled with BD566-HTL substrate==

== Structural highlights ==

<table><tr><td colspan='2'>[[21dt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia Escherichia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=21DT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=21DT 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]] 1.48Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1EQX:2-[3,6-bis[(1~{R},5~{S})-3-oxa-8-azabicyclo[3.2.1]octan-8-yl]-1~{H}-xanthen-9-yl]-4-[2-(2-hexoxyethoxy)ethylcarbamoyl]benzoic+acid'>A1EQX</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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=21dt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=21dt OCA], [https://pdbe.org/21dt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=21dt RCSB], [https://www.ebi.ac.uk/pdbsum/21dt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=21dt ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Self-labeling protein tags (SLPs) enable protein-specific conjugation of synthetic fluorophores for versatile bioimaging, yet their rational engineering has largely relied on static structural models. Here, we reveal that crystal structures of SLP-dye complexes generally bear packing artifacts due to strong pi-pi interactions of dyes, frequently failing to profile the chromophore microenvironment. By integrating molecular dynamics (MD) with crystallography, we elucidate distinct dynamic behaviors of fluorophores across major SLPs: quasi-free diffusion in SNAP-tag, balanced hydrophobic-polar interactions in TMP-tag, and discrete, state-selective anchoring in HaloTag and Rho-tag. Comparisons with the newly developed SNAP-tag2 demonstrate that functional evolution reshapes conformational landscapes rather than merely strengthening binding. We further validate simulation-derived predictions through MD-guided lattice selection. Together, this work establishes a comparative, dynamic framework for understanding SLP-dye interactions beyond crystallography, while providing a conceptual basis for further engineering chemigenetic tools for advanced imaging and sensing.

~~Authors:~~ Zhang, K., Chen, Z.

Dynamic conformations of fluorophores on self-labeling protein tags.,Zhang K, Zhang J, Chen N, Chen Z Biophys J. 2026 Jun 26:S0006-3495(26)00459-5. doi: 10.1016/j.bpj.2026.06.033. PMID:42363595<ref>PMID:42363595</ref>

~~Description: X-ray structure~~ of the ~~Haloalkane dehalogenase HaloTag7 labeled with BD566~~-~~HTL substrate~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased Structures~~]]

</div>

[[Category: ~~Zhang, K~~]]

[[Category: Chen, Z]]

== References ==

__TOC__

</StructureSection>

[[Category: Escherichia]]

[[Category: Large Structures]]

[[Category: Chen Z]]

[[Category: Zhang K]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 21dt is ON HOLD  until Paper Publication
+==X-ray structure of the Haloalkane dehalogenase HaloTag7 labeled with BD566-HTL substrate==
+<StructureSection load='21dt' size='340' side='right'caption='[[21dt]], [[Resolution|resolution]] 1.48&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[21dt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia Escherichia]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=21DT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=21DT 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]] 1.48&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1EQX:2-[3,6-bis[(1~{R},5~{S})-3-oxa-8-azabicyclo[3.2.1]octan-8-yl]-1~{H}-xanthen-9-yl]-4-[2-(2-hexoxyethoxy)ethylcarbamoyl]benzoic+acid'>A1EQX</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GLC:ALPHA-D-GLUCOSE'>GLC</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=21dt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=21dt OCA], [https://pdbe.org/21dt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=21dt RCSB], [https://www.ebi.ac.uk/pdbsum/21dt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=21dt ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Self-labeling protein tags (SLPs) enable protein-specific conjugation of synthetic fluorophores for versatile bioimaging, yet their rational engineering has largely relied on static structural models. Here, we reveal that crystal structures of SLP-dye complexes generally bear packing artifacts due to strong pi-pi interactions of dyes, frequently failing to profile the chromophore microenvironment. By integrating molecular dynamics (MD) with crystallography, we elucidate distinct dynamic behaviors of fluorophores across major SLPs: quasi-free diffusion in SNAP-tag, balanced hydrophobic-polar interactions in TMP-tag, and discrete, state-selective anchoring in HaloTag and Rho-tag. Comparisons with the newly developed SNAP-tag2 demonstrate that functional evolution reshapes conformational landscapes rather than merely strengthening binding. We further validate simulation-derived predictions through MD-guided lattice selection. Together, this work establishes a comparative, dynamic framework for understanding SLP-dye interactions beyond crystallography, while providing a conceptual basis for further engineering chemigenetic tools for advanced imaging and sensing.
-Authors: Zhang, K., Chen, Z.
+Dynamic conformations of fluorophores on self-labeling protein tags.,Zhang K, Zhang J, Chen N, Chen Z Biophys J. 2026 Jun 26:S0006-3495(26)00459-5. doi: 10.1016/j.bpj.2026.06.033. PMID:42363595<ref>PMID:42363595</ref>
-Description: X-ray structure of the Haloalkane dehalogenase HaloTag7 labeled with BD566-HTL substrate
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Zhang, K]]
+<div class="pdbe-citations 21dt" style="background-color:#fffaf0;"></div>
-[[Category: Chen, Z]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia]]
+[[Category: Large Structures]]
+[[Category: Chen Z]]
+[[Category: Zhang K]]