https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=OCAProteopedia - User contributions [en]2026-09-15T13:51:58ZUser contributionsMediaWiki 1.43.8https://proteopedia.org/index.php?title=Dihydropoyl_dehydrogenase&diff=4490173Dihydropoyl dehydrogenase2026-09-14T15:10:51Z<p>OCA: Create redirect page</p>
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<div>#REDIRECT[[Pyruvate_dehydrogenase]]</div>OCAhttps://proteopedia.org/index.php?title=Dlta-1-pyrroline-5-carboxylate_dehydrogenase&diff=4490172Dlta-1-pyrroline-5-carboxylate dehydrogenase2026-09-14T15:10:47Z<p>OCA: Create redirect page</p>
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<div>#REDIRECT[[Pyrroline-5-carboxylate_dehydrogenase]]</div>OCAhttps://proteopedia.org/index.php?title=C-glucosyl_oxidoreductase&diff=4490171C-glucosyl oxidoreductase2026-09-14T15:10:44Z<p>OCA: Create redirect page</p>
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<div>#REDIRECT[[Pyranose_oxidase]]</div>OCAhttps://proteopedia.org/index.php?title=Calcium-activated_neutral_protein&diff=4490170Calcium-activated neutral protein2026-09-14T15:10:39Z<p>OCA: Create redirect page</p>
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<div>#REDIRECT[[Proteinase]]</div>OCAhttps://proteopedia.org/index.php?title=HAB1&diff=4490169HAB12026-09-14T15:10:22Z<p>OCA: Create redirect page</p>
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<div>#REDIRECT[[Protein_phosphatase]]</div>OCAhttps://proteopedia.org/index.php?title=Pyruvate_dehydrogenase_phosphatase&diff=4490168Pyruvate dehydrogenase phosphatase2026-09-14T15:10:21Z<p>OCA: Create redirect page</p>
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<div>#REDIRECT[[Protein_phosphatase]]</div>OCAhttps://proteopedia.org/index.php?title=Spinophilin&diff=4490167Spinophilin2026-09-14T15:10:17Z<p>OCA: Create redirect page</p>
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<div>#REDIRECT[[Protein_phosphatase]]</div>OCAhttps://proteopedia.org/index.php?title=Neurabin-2&diff=4490166Neurabin-22026-09-14T15:10:13Z<p>OCA: Create redirect page</p>
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<div>#REDIRECT[[Protein_phosphatase]]</div>OCAhttps://proteopedia.org/index.php?title=Neurabin-1&diff=4490165Neurabin-12026-09-14T15:10:13Z<p>OCA: Create redirect page</p>
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<div>#REDIRECT[[Protein_phosphatase]]</div>OCAhttps://proteopedia.org/index.php?title=Parkinson_disease_protein_7&diff=4490164Parkinson disease protein 72026-09-14T15:08:36Z<p>OCA: Create redirect page</p>
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<div>#REDIRECT[[Protein_DJ-1]]</div>OCAhttps://proteopedia.org/index.php?title=Category:Desulfuromonas_soudanensis&diff=4490147Category:Desulfuromonas soudanensis2026-09-09T08:34:12Z<p>OCA: Protected "Category:Desulfuromonas soudanensis": Seeded page ([Edit=Allow only administrators] (indefinite) [Move=Allow only administrators] (indefinite))</p>
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<div>List of pages with the keyword Desulfuromonas soudanensis</div>OCAhttps://proteopedia.org/index.php?title=Category:Desulfuromonas_soudanensis&diff=4490146Category:Desulfuromonas soudanensis2026-09-09T08:34:11Z<p>OCA: Created page with "List of pages with the keyword Desulfuromonas soudanensis"</p>
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<div>List of pages with the keyword Desulfuromonas soudanensis</div>OCAhttps://proteopedia.org/index.php?title=9yuq&diff=44901459yuq2026-09-09T08:34:11Z<p>OCA: </p>
<hr />
<div><br />
==A Bundled Antiparallel Cytochrome Nanowire Produced by Desulfuromonas soudanensis WTL==<br />
<StructureSection load='9yuq' size='340' side='right'caption='[[9yuq]], [[Resolution|resolution]] 3.11&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[9yuq]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Desulfuromonas_soudanensis Desulfuromonas soudanensis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9YUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9YUQ FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.11&#8491;</td></tr><br />
<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=HEC:HEME+C'>HEC</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9yuq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9yuq OCA], [https://pdbe.org/9yuq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9yuq RCSB], [https://www.ebi.ac.uk/pdbsum/9yuq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9yuq ProSAT]</span></td></tr><br />
</table><br />
__TOC__<br />
</StructureSection><br />
[[Category: Desulfuromonas soudanensis]]<br />
[[Category: Large Structures]]<br />
[[Category: Bond DR]]<br />
[[Category: Chan CH]]<br />
[[Category: Petersen HA]]<br />
[[Category: Wang F]]</div>OCAhttps://proteopedia.org/index.php?title=9t8s&diff=44901449t8s2026-09-09T08:30:33Z<p>OCA: </p>
<hr />
<div><br />
==E. coli 70S ribosome from delta-10 strain, PTC class 8==<br />
<StructureSection load='9t8s' size='340' side='right'caption='[[9t8s]], [[Resolution|resolution]] 2.22&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[9t8s]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9T8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9T8S FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.22&#8491;</td></tr><br />
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=3TD:(1S)-1,4-ANHYDRO-1-(3-METHYL-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-5-O-PHOSPHONO-D-RIBITOL'>3TD</scene>, <scene name='pdbligand=4D4:(2S,3R)-2-AZANYL-5-CARBAMIMIDAMIDO-3-OXIDANYL-PENTANOIC+ACID'>4D4</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MEQ:N5-METHYLGLUTAMINE'>MEQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MS6:(2~{S})-2-azanyl-4-methylsulfanyl-butanethioic+O-acid'>MS6</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SR0:4-azaniumylbutyl(3-azaniumylpropyl)azanium'>SR0</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9t8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9t8s OCA], [https://pdbe.org/9t8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9t8s RCSB], [https://www.ebi.ac.uk/pdbsum/9t8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9t8s ProSAT]</span></td></tr><br />
</table><br />
__TOC__<br />
</StructureSection><br />
[[Category: Escherichia coli]]<br />
[[Category: Large Structures]]<br />
[[Category: Larsson DSD]]<br />
[[Category: Selmer M]]</div>OCAhttps://proteopedia.org/index.php?title=9t8r&diff=44901439t8r2026-09-09T08:30:32Z<p>OCA: </p>
<hr />
<div><br />
==E. coli 70S ribosome from delta-10 strain, PTC class 7==<br />
<StructureSection load='9t8r' size='340' side='right'caption='[[9t8r]], [[Resolution|resolution]] 2.22&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[9t8r]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9T8R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9T8R FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.22&#8491;</td></tr><br />
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1MG:1N-METHYLGUANOSINE-5-MONOPHOSPHATE'>1MG</scene>, <scene name='pdbligand=2MG:2N-METHYLGUANOSINE-5-MONOPHOSPHATE'>2MG</scene>, <scene name='pdbligand=3TD:(1S)-1,4-ANHYDRO-1-(3-METHYL-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL)-5-O-PHOSPHONO-D-RIBITOL'>3TD</scene>, <scene name='pdbligand=4D4:(2S,3R)-2-AZANYL-5-CARBAMIMIDAMIDO-3-OXIDANYL-PENTANOIC+ACID'>4D4</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=6MZ:N6-METHYLADENOSINE-5-MONOPHOSPHATE'>6MZ</scene>, <scene name='pdbligand=H2U:5,6-DIHYDROURIDINE-5-MONOPHOSPHATE'>H2U</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MEQ:N5-METHYLGLUTAMINE'>MEQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MS6:(2~{S})-2-azanyl-4-methylsulfanyl-butanethioic+O-acid'>MS6</scene>, <scene name='pdbligand=OMC:O2-METHYLYCYTIDINE-5-MONOPHOSPHATE'>OMC</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=SR0:N~1~-(3-azaniumylpropyl)butane-1,4-diaminium'>SR0</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9t8r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9t8r OCA], [https://pdbe.org/9t8r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9t8r RCSB], [https://www.ebi.ac.uk/pdbsum/9t8r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9t8r ProSAT]</span></td></tr><br />
</table><br />
__TOC__<br />
</StructureSection><br />
[[Category: Escherichia coli]]<br />
[[Category: Large Structures]]<br />
[[Category: Larsson DSD]]<br />
[[Category: Selmer M]]</div>OCAhttps://proteopedia.org/index.php?title=Category:Schut_G&diff=4490142Category:Schut G2026-09-09T08:27:56Z<p>OCA: Protected "Category:Schut G": Seeded page ([Edit=Allow only administrators] (indefinite) [Move=Allow only administrators] (indefinite))</p>
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<div>List of pages with the keyword Schut G</div>OCAhttps://proteopedia.org/index.php?title=Category:Schut_G&diff=4490141Category:Schut G2026-09-09T08:27:55Z<p>OCA: Created page with "List of pages with the keyword Schut G"</p>
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<div>List of pages with the keyword Schut G</div>OCAhttps://proteopedia.org/index.php?title=Category:Haloferax_volcanii&diff=4490140Category:Haloferax volcanii2026-09-09T08:27:52Z<p>OCA: Protected "Category:Haloferax volcanii": Seeded page ([Edit=Allow only administrators] (indefinite) [Move=Allow only administrators] (indefinite))</p>
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<div>List of pages with the keyword Haloferax volcanii</div>OCAhttps://proteopedia.org/index.php?title=9q1t&diff=44901399q1t2026-09-09T08:27:51Z<p>OCA: </p>
<hr />
<div><br />
==1.9 Angstrom crystal structure of the tungsten-dependent aldehyde oxidoreductase WOR83 from Haloferax volcanii==<br />
<StructureSection load='9q1t' size='340' side='right'caption='[[9q1t]], [[Resolution|resolution]] 1.87&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[9q1t]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloferax_volcanii Haloferax volcanii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9Q1T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9Q1T FirstGlance]. <br><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]] 1.87&#8491;</td></tr><br />
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=58M:bis[(5aR,8R,9aR)-2-amino-4-oxo-8-[(phosphonooxy)methyl]-3,5,5a,8,9a,10-hexahydro-4H-pyrano[3,2-g]pteridine-6,7-bis(thiolato)-kappa~2~S~6~,S~7~]tungsten'>58M</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9q1t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9q1t OCA], [https://pdbe.org/9q1t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9q1t RCSB], [https://www.ebi.ac.uk/pdbsum/9q1t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9q1t ProSAT]</span></td></tr><br />
</table><br />
__TOC__<br />
</StructureSection><br />
[[Category: Haloferax volcanii]]<br />
[[Category: Large Structures]]<br />
[[Category: Adams MWW]]<br />
[[Category: Lanzilotta WN]]<br />
[[Category: Schut G]]</div>OCAhttps://proteopedia.org/index.php?title=9q0n&diff=44901389q0n2026-09-09T08:27:36Z<p>OCA: </p>
<hr />
<div><br />
==Cryo-EM structure of PPAT-NUDT5 complex bound to 6-methylthioinosine-5'-monophosphate (6-meTIMP)==<br />
<StructureSection load='9q0n' size='340' side='right'caption='[[9q0n]], [[Resolution|resolution]] 2.80&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[9q0n]] is a 8 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=9Q0N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9Q0N FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.8&#8491;</td></tr><br />
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1CQ3:6-(methylsulfanyl)-9-(5-O-phosphono-beta-D-ribofuranosyl)-9H-purine'>A1CQ3</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9q0n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9q0n OCA], [https://pdbe.org/9q0n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9q0n RCSB], [https://www.ebi.ac.uk/pdbsum/9q0n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9q0n ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[https://www.uniprot.org/uniprot/PUR1_HUMAN PUR1_HUMAN] Catalyzes the formation of phosphoribosylamine from phosphoribosylpyrophosphate (PRPP) and glutamine.[UniProtKB:P35433]<br />
__TOC__<br />
</StructureSection><br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Rape M]]<br />
[[Category: Witus SRW]]<br />
[[Category: Yang Z]]</div>OCAhttps://proteopedia.org/index.php?title=9pa0&diff=44901379pa02026-09-09T08:27:23Z<p>OCA: </p>
<hr />
<div><br />
==Hybrid-1 form of human telomere DNA quadruplex with wild-type 5'-flanking in K+ solution==<br />
<StructureSection load='9pa0' size='340' side='right'caption='[[9pa0]]' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[9pa0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9PA0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9PA0 FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, models</td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9pa0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9pa0 OCA], [https://pdbe.org/9pa0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9pa0 RCSB], [https://www.ebi.ac.uk/pdbsum/9pa0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9pa0 ProSAT]</span></td></tr><br />
</table><br />
__TOC__<br />
</StructureSection><br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Dickerhoff J]]<br />
[[Category: Yang D]]</div>OCAhttps://proteopedia.org/index.php?title=Category:Schistosoma&diff=4490136Category:Schistosoma2026-09-09T08:24:16Z<p>OCA: Protected "Category:Schistosoma": Seeded page ([Edit=Allow only administrators] (indefinite) [Move=Allow only administrators] (indefinite))</p>
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<div>List of pages with the keyword Schistosoma</div>OCAhttps://proteopedia.org/index.php?title=8hhy&diff=44901358hhy2026-09-09T08:23:34Z<p>OCA: </p>
<hr />
<div><br />
==SARS-CoV-2 Delta Spike in complex with IS-9A==<br />
<StructureSection load='8hhy' size='340' side='right'caption='[[8hhy]], [[Resolution|resolution]] 2.77&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[8hhy]] is a 9 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Severe_acute_respiratory_syndrome_coronavirus_2 Severe acute respiratory syndrome coronavirus 2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8HHY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8HHY FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.77&#8491;</td></tr><br />
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8hhy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8hhy OCA], [https://pdbe.org/8hhy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8hhy RCSB], [https://www.ebi.ac.uk/pdbsum/8hhy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8hhy ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[https://www.uniprot.org/uniprot/SPIKE_SARS2 SPIKE_SARS2] attaches the virion to the cell membrane by interacting with host receptor, initiating the infection (By similarity). Binding to human ACE2 receptor and internalization of the virus into the endosomes of the host cell induces conformational changes in the Spike glycoprotein (PubMed:32142651, PubMed:32075877, PubMed:32155444). Uses also human TMPRSS2 for priming in human lung cells which is an essential step for viral entry (PubMed:32142651). Proteolysis by cathepsin CTSL may unmask the fusion peptide of S2 and activate membranes fusion within endosomes.[HAMAP-Rule:MF_04099]<ref>PMID:32075877</ref> <ref>PMID:32142651</ref> <ref>PMID:32155444</ref> mediates fusion of the virion and cellular membranes by acting as a class I viral fusion protein. Under the current model, the protein has at least three conformational states: pre-fusion native state, pre-hairpin intermediate state, and post-fusion hairpin state. During viral and target cell membrane fusion, the coiled coil regions (heptad repeats) assume a trimer-of-hairpins structure, positioning the fusion peptide in close proximity to the C-terminal region of the ectodomain. The formation of this structure appears to drive apposition and subsequent fusion of viral and target cell membranes.[HAMAP-Rule:MF_04099] Acts as a viral fusion peptide which is unmasked following S2 cleavage occurring upon virus endocytosis.[HAMAP-Rule:MF_04099]<br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
Antibody-mediated immunity plays a crucial role in protection against SARS-CoV-2 infection. We isolated a panel of neutralizing anti-receptor-binding domain (RBD) antibodies elicited upon natural infection and vaccination and showed that they recognize an immunogenic patch on the internal surface of the core RBD, which faces inwards and is hidden in the "down" state. These antibodies broadly neutralize wild type (Wuhan-Hu-1) SARS-CoV-2, Beta and Delta variants and some are effective against other sarbecoviruses. We observed a continuum of partially overlapping antibody epitopes from lower to upper part of the inner face of the RBD and some antibodies extend towards the receptor-binding motif. The majority of antibodies are substantially compromised by three mutational hotspots (S371L/F, S373P and S375F) in the lower part of the Omicron BA.1, BA.2 and BA.4/5 RBD. By contrast, antibody IY-2A induces a partial unfolding of this variable region and interacts with a conserved conformational epitope to tolerate all antigenic variations and neutralize diverse sarbecoviruses as well. This finding establishes that antibody recognition is not limited to the normal surface structures on the RBD. In conclusion, the delineation of functionally and structurally conserved RBD epitopes highlights potential vaccine and therapeutic candidates for COVID-19.<br />
<br />
Structural basis for a conserved neutralization epitope on the receptor-binding domain of SARS-CoV-2.,Huang KA, Chen X, Mohapatra A, Nguyen HTV, Schimanski L, Tan TK, Rijal P, Vester SK, Hills RA, Howarth M, Keeffe JR, Cohen AA, Kakutani LM, Wu YM, Shahed-Al-Mahmud M, Chou YC, Bjorkman PJ, Townsend AR, Ma C Nat Commun. 2023 Jan 19;14(1):311. doi: 10.1038/s41467-023-35949-8. PMID:36658148<ref>PMID:36658148</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 8hhy" style="background-color:#fffaf0;"></div><br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Severe acute respiratory syndrome coronavirus 2]]<br />
[[Category: Mohapatra A]]<br />
[[Category: Wu Y-M]]</div>OCAhttps://proteopedia.org/index.php?title=7vu1&diff=44901347vu12026-09-09T08:23:00Z<p>OCA: </p>
<hr />
<div><br />
==Chitoporin from Escherichia coli complex with chitohexaose==<br />
<StructureSection load='7vu1' size='340' side='right'caption='[[7vu1]], [[Resolution|resolution]] 1.90&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[7vu1]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VU1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VU1 FirstGlance]. <br><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]] 1.9&#8491;</td></tr><br />
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=DMU:DECYL-BETA-D-MALTOPYRANOSIDE'>DMU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7vu1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vu1 OCA], [https://pdbe.org/7vu1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vu1 RCSB], [https://www.ebi.ac.uk/pdbsum/7vu1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vu1 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[https://www.uniprot.org/uniprot/CHIP_ECOLI CHIP_ECOLI] Involved in the uptake of chitosugars.<ref>PMID:16857666</ref> <ref>PMID:19682266</ref> <br />
<br />
==See Also==<br />
*[[Porin 3D structures|Porin 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Escherichia coli K-12]]<br />
[[Category: Large Structures]]<br />
[[Category: Amornloetwattana R]]<br />
[[Category: Soysa HSM]]<br />
[[Category: Suginta W]]<br />
[[Category: Van den Berg B]]</div>OCAhttps://proteopedia.org/index.php?title=7vu0&diff=44901337vu02026-09-09T08:22:59Z<p>OCA: </p>
<hr />
<div><br />
==Chitoporin from Escherichia coli==<br />
<StructureSection load='7vu0' size='340' side='right'caption='[[7vu0]], [[Resolution|resolution]] 1.85&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[7vu0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VU0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VU0 FirstGlance]. <br><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]] 1.85&#8491;</td></tr><br />
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=DMU:DECYL-BETA-D-MALTOPYRANOSIDE'>DMU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7vu0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vu0 OCA], [https://pdbe.org/7vu0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vu0 RCSB], [https://www.ebi.ac.uk/pdbsum/7vu0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vu0 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[https://www.uniprot.org/uniprot/CHIP_ECOLI CHIP_ECOLI] Involved in the uptake of chitosugars.<ref>PMID:16857666</ref> <ref>PMID:19682266</ref> <br />
<br />
==See Also==<br />
*[[Porin 3D structures|Porin 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Escherichia coli K-12]]<br />
[[Category: Large Structures]]<br />
[[Category: Amornloetwattana R]]<br />
[[Category: Soysa HSM]]<br />
[[Category: Suginta W]]<br />
[[Category: Van den Berg B]]</div>OCAhttps://proteopedia.org/index.php?title=7vtz&diff=44901327vtz2026-09-09T08:22:54Z<p>OCA: </p>
<hr />
<div><br />
==Chitoporin from Escherichia coli==<br />
<StructureSection load='7vtz' size='340' side='right'caption='[[7vtz]], [[Resolution|resolution]] 2.10&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[7vtz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7VTZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7VTZ FirstGlance]. <br><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]] 2.1&#8491;</td></tr><br />
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=PT:PLATINUM+(II)+ION'>PT</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7vtz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7vtz OCA], [https://pdbe.org/7vtz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7vtz RCSB], [https://www.ebi.ac.uk/pdbsum/7vtz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7vtz ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[https://www.uniprot.org/uniprot/CHIP_ECOLI CHIP_ECOLI] Involved in the uptake of chitosugars.<ref>PMID:16857666</ref> <ref>PMID:19682266</ref> <br />
<br />
==See Also==<br />
*[[Porin 3D structures|Porin 3D structures]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Escherichia coli K-12]]<br />
[[Category: Large Structures]]<br />
[[Category: Amornloetwattana R]]<br />
[[Category: Soysa HSM]]<br />
[[Category: Suginta W]]<br />
[[Category: Van den Berg B]]</div>OCAhttps://proteopedia.org/index.php?title=7pq2&diff=44901317pq22026-09-09T08:22:44Z<p>OCA: </p>
<hr />
<div><br />
==Crystal Structure of the Ring Nuclease 0811 from Sulfolobus islandicus (Sis0811) in its apo form==<br />
<StructureSection load='7pq2' size='340' side='right'caption='[[7pq2]], [[Resolution|resolution]] 2.38&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7PQ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7PQ2 FirstGlance]. <br><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]] 2.38&#8491;</td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7pq2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7pq2 OCA], [https://pdbe.org/7pq2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7pq2 RCSB], [https://www.ebi.ac.uk/pdbsum/7pq2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7pq2 ProSAT]</span></td></tr><br />
</table><br />
__TOC__<br />
</StructureSection><br />
[[Category: Large Structures]]<br />
[[Category: Jensen ALG]]<br />
[[Category: Lopez-Mendez B]]<br />
[[Category: Marchena-Hurtado J]]<br />
[[Category: Molina R]]<br />
[[Category: Montoya G]]<br />
[[Category: Stella S]]</div>OCAhttps://proteopedia.org/index.php?title=7lgr&diff=44901307lgr2026-09-09T08:22:41Z<p>OCA: </p>
<hr />
<div><br />
==Streptococcus mutans Collagen binding Protein CNM - N2 Domain==<br />
<StructureSection load='7lgr' size='340' side='right'caption='[[7lgr]], [[Resolution|resolution]] 1.60&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7LGR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7LGR FirstGlance]. <br><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]] 1.6&#8491;</td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7lgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7lgr OCA], [https://pdbe.org/7lgr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7lgr RCSB], [https://www.ebi.ac.uk/pdbsum/7lgr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7lgr ProSAT]</span></td></tr><br />
</table><br />
<br />
==See Also==<br />
*[[Adhesin 3D structures|Adhesin 3D structures]]<br />
__TOC__<br />
</StructureSection><br />
[[Category: Large Structures]]<br />
[[Category: Deivanayagam C]]<br />
[[Category: Schormann N]]</div>OCAhttps://proteopedia.org/index.php?title=6hb8&diff=44901296hb82026-09-09T08:22:21Z<p>OCA: </p>
<hr />
<div><br />
==Crystal structure of OXA-517 beta-lactamase==<br />
<StructureSection load='6hb8' size='340' side='right'caption='[[6hb8]], [[Resolution|resolution]] 1.86&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[6hb8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6HB8 FirstGlance]. <br><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]] 1.86&#8491;</td></tr><br />
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ETX:2-ETHOXYETHANOL'>ETX</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6hb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hb8 OCA], [https://pdbe.org/6hb8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6hb8 RCSB], [https://www.ebi.ac.uk/pdbsum/6hb8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6hb8 ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[https://www.uniprot.org/uniprot/A0A1U8YI81_KLEPN A0A1U8YI81_KLEPN] <br />
<br />
==See Also==<br />
*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]<br />
__TOC__<br />
</StructureSection><br />
[[Category: Klebsiella pneumoniae]]<br />
[[Category: Large Structures]]<br />
[[Category: Dabos L]]<br />
[[Category: Iorga B]]<br />
[[Category: Jaskolski M]]<br />
[[Category: Naas T]]<br />
[[Category: Raczynska JE]]<br />
[[Category: Retailleau P]]<br />
[[Category: Zavala A]]</div>OCAhttps://proteopedia.org/index.php?title=2w8y&diff=44901282w8y2026-09-09T08:20:08Z<p>OCA: </p>
<hr />
<div><br />
==RU486 bound to the progesterone receptor in a destabilized agonistic conformation==<br />
<StructureSection load='2w8y' size='340' side='right'caption='[[2w8y]], [[Resolution|resolution]] 1.80&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[2w8y]] 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=2W8Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W8Y FirstGlance]. <br><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]] 1.8&#8491;</td></tr><br />
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=486:11-(4-DIMETHYLAMINO-PHENYL)-17-HYDROXY-13-METHYL-17-PROP-1-YNYL-1,2,6,7,8,11,12,13,14,15,16,17-DODEC+AHYDRO-CYCLOPENTA[A]PHENANTHREN-3-ONE'>486</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=NDR:(14BETA,17ALPHA)-17-ETHYNYL-17-HYDROXYESTR-4-EN-3-ONE'>NDR</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2w8y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w8y OCA], [https://pdbe.org/2w8y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w8y RCSB], [https://www.ebi.ac.uk/pdbsum/2w8y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w8y ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[https://www.uniprot.org/uniprot/PRGR_HUMAN PRGR_HUMAN] The steroid hormones and their receptors are involved in the regulation of eukaryotic gene expression and affect cellular proliferation and differentiation in target tissues. Progesterone receptor isoform B (PRB) is involved activation of c-SRC/MAPK signaling on hormone stimulation.<ref>PMID:15572662</ref> <ref>PMID:15798179</ref> <ref>PMID:17020914</ref> <ref>PMID:17347654</ref> <ref>PMID:17717077</ref> <ref>PMID:17173941</ref> <ref>PMID:18202149</ref> Isoform A is inactive in stimulating c-Src/MAPK signaling on hormone stimulation.<ref>PMID:15572662</ref> <ref>PMID:15798179</ref> <ref>PMID:17020914</ref> <ref>PMID:17347654</ref> <ref>PMID:17717077</ref> <ref>PMID:17173941</ref> <ref>PMID:18202149</ref> <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/w8/2w8y_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</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=2w8y ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
Here we describe the 1.95 A structure of the clinically used antiprogestin RU486 (mifepristone) in complex with the progesterone receptor (PR). The structure was obtained by taking a crystal of the PR ligand binding domain containing the agonist norethindrone and soaking it in a solution containing the antagonist RU486 for extended times. Clear ligand exchange could be observed in one copy of the PR ligand binding domain dimer in the crystal. RU486 binds while PR is in an agonistic conformation without displacing helix 12. Although this is probably because of the constraints of the crystal lattice, it demonstrates that helix 12 displacement is not a prerequisite for RU486 binding. Interestingly, B-factor analysis clearly shows that helix 12 becomes more flexible after RU486 binding, suggesting that RU486, being a model antagonist, does not induce one fixed conformation of helix 12 but changes its positional equilibrium. This conclusion is confirmed by comparing the structures of RU486 bound to PR and RU486 bound to the glucocorticoid receptor.<br />
<br />
The X-ray structure of RU486 bound to the progesterone receptor in a destabilized agonistic conformation.,Raaijmakers HC, Versteegh JE, Uitdehaag JC J Biol Chem. 2009 Jul 17;284(29):19572-9. Epub 2009 Apr 16. PMID:19372222<ref>PMID:19372222</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 2w8y" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Progesterone receptor|Progesterone receptor]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Raaijmakers HCA]]<br />
[[Category: Uitdehaag JCM]]<br />
[[Category: Versteeg J]]</div>OCAhttps://proteopedia.org/index.php?title=Category:Bobileva_O&diff=4490127Category:Bobileva O2026-09-09T08:20:03Z<p>OCA: Protected "Category:Bobileva O": Seeded page ([Edit=Allow only administrators] (indefinite) [Move=Allow only administrators] (indefinite))</p>
<hr />
<div>List of pages with the keyword Bobileva O</div>OCAhttps://proteopedia.org/index.php?title=Category:Bobileva_O&diff=4490126Category:Bobileva O2026-09-09T08:20:03Z<p>OCA: Created page with "List of pages with the keyword Bobileva O"</p>
<hr />
<div>List of pages with the keyword Bobileva O</div>OCAhttps://proteopedia.org/index.php?title=29ge&diff=449012529ge2026-09-09T08:20:00Z<p>OCA: </p>
<hr />
<div><br />
==Crystal structure of human METTL1 in complex with OBV617 (compound B19)==<br />
<StructureSection load='29ge' size='340' side='right'caption='[[29ge]], [[Resolution|resolution]] 2.89&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[29ge]] is a 1 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=29GE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=29GE FirstGlance]. <br><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]] 2.89&#8491;</td></tr><br />
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1J17:[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-[4-[[2,4-bis(oxidanyl)phenyl]methyl]piperazin-1-yl]methanone'>A1J17</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=29ge FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=29ge OCA], [https://pdbe.org/29ge PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=29ge RCSB], [https://www.ebi.ac.uk/pdbsum/29ge PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=29ge ProSAT]</span></td></tr><br />
</table><br />
__TOC__<br />
</StructureSection><br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Bobileva O]]<br />
[[Category: Caflisch A]]<br />
[[Category: Nai F]]</div>OCAhttps://proteopedia.org/index.php?title=26qi&diff=449012426qi2026-09-09T08:19:11Z<p>OCA: </p>
<hr />
<div><br />
==Cryo-EM structure of human UGCG bound to Ibiglustat==<br />
<StructureSection load='26qi' size='340' side='right'caption='[[26qi]], [[Resolution|resolution]] 3.43&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[26qi]] is a 1 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=26QI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=26QI FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.43&#8491;</td></tr><br />
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KYF:(1R,3S,4R)-1-azabicyclo[2.2.2]octan-3-yl+{2-[2-(4-fluorophenyl)-1,3-thiazol-4-yl]propan-2-yl}carbamate'>KYF</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=26qi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=26qi OCA], [https://pdbe.org/26qi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=26qi RCSB], [https://www.ebi.ac.uk/pdbsum/26qi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=26qi ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[https://www.uniprot.org/uniprot/CEGT_HUMAN CEGT_HUMAN] Participates in the initial step of the glucosylceramide-based glycosphingolipid/GSL synthetic pathway at the cytosolic surface of the Golgi (PubMed:1532799, PubMed:8643456). Catalyzes the transfer of glucose from UDP-glucose to ceramide to produce glucosylceramide/GlcCer (such as beta-D-glucosyl-(1<->1')-N-acylsphing-4-enine) (PubMed:1532799, PubMed:8643456). GlcCer is the core component of glycosphingolipids/GSLs, amphipathic molecules consisting of a ceramide lipid moiety embedded in the outer leaflet of the membrane, linked to one of hundreds of different externally oriented oligosaccharide structures (PubMed:8643456). Glycosphingolipids are essential components of membrane microdomains that mediate membrane trafficking and signal transduction, implicated in many fundamental cellular processes, including growth, differentiation, migration, morphogenesis, cell-to-cell and cell-to-matrix interactions (By similarity). They are required for instance in the proper development and functioning of the nervous system (By similarity). As an example of their role in signal transduction, they regulate the leptin receptor/LEPR in the leptin-mediated signaling pathway (By similarity). They also play an important role in the establishment of the skin barrier regulating keratinocyte differentiation and the proper assembly of the cornified envelope (By similarity). The biosynthesis of GSLs is also required for the proper intestinal endocytic uptake of nutritional lipids (By similarity). Catalyzes the synthesis of xylosylceramide/XylCer (such as beta-D-xylosyl-(1<->1')-N-acylsphing-4-enine) using UDP-Xyl as xylose donor (PubMed:33361282).[UniProtKB:O88693]<ref>PMID:1532799</ref> <ref>PMID:33361282</ref> <ref>PMID:8643456</ref> <ref>PMID:8643456</ref> <br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Cao Z]]<br />
[[Category: Guo X]]<br />
[[Category: Hu W]]<br />
[[Category: Jiang M]]<br />
[[Category: Jiang Y]]<br />
[[Category: Jin S]]<br />
[[Category: Li C]]<br />
[[Category: Li Y]]<br />
[[Category: Wang JJ]]<br />
[[Category: Wang MW]]<br />
[[Category: Wu C]]<br />
[[Category: Xu HE]]<br />
[[Category: Xu J]]<br />
[[Category: Xu Y]]<br />
[[Category: Yuan Q]]</div>OCAhttps://proteopedia.org/index.php?title=25sb&diff=449012325sb2026-09-09T08:18:33Z<p>OCA: </p>
<hr />
<div><br />
==CyroEM structure of the complex between Shiga toxin Stx1a B subunit and neutralising Fab fragment of RDS059==<br />
<StructureSection load='25sb' size='340' side='right'caption='[[25sb]], [[Resolution|resolution]] 2.00&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[25sb]] is a 15 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=25SB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=25SB FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2&#8491;</td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=25sb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=25sb OCA], [https://pdbe.org/25sb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=25sb RCSB], [https://www.ebi.ac.uk/pdbsum/25sb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=25sb ProSAT]</span></td></tr><br />
</table><br />
__TOC__<br />
</StructureSection><br />
[[Category: Escherichia coli O157:H7]]<br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Chen SD]]<br />
[[Category: Li X]]</div>OCAhttps://proteopedia.org/index.php?title=22xc&diff=449012222xc2026-09-09T08:15:51Z<p>OCA: </p>
<hr />
<div><br />
==Structure of CXCR4 in complex with a de-novo designed mini-protein antagonist==<br />
<StructureSection load='22xc' size='340' side='right'caption='[[22xc]], [[Resolution|resolution]] 3.28&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[22xc]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=22XC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=22XC FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.28&#8491;</td></tr><br />
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CLR:CHOLESTEROL'>CLR</scene>, <scene name='pdbligand=D21:[(2~{R})-1-hexadecanoyloxy-3-phosphonooxy-propan-2-yl]+octadec-9-enoate'>D21</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=22xc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=22xc OCA], [https://pdbe.org/22xc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=22xc RCSB], [https://www.ebi.ac.uk/pdbsum/22xc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=22xc ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[https://www.uniprot.org/uniprot/CXCR4_HUMAN CXCR4_HUMAN] Defects in CXCR4 are a cause of WHIM syndrome (WHIM) [MIM:[https://omim.org/entry/193670 193670]; also known as warts, hypogammaglobulinemia, infections and myelokathexis. WHIM syndrome is an immunodeficiency disease characterized by neutropenia, hypogammaglobulinemia and extensive human papillomavirus (HPV) infection. Despite the peripheral neutropenia, bone marrow aspirates from affected individuals contain abundant mature myeloid cells, a condition termed myelokathexis.<ref>PMID:12692554</ref> <br />
== Function ==<br />
[https://www.uniprot.org/uniprot/CXCR4_HUMAN CXCR4_HUMAN] Receptor for the C-X-C chemokine CXCL12/SDF-1 that transduces a signal by increasing intracellular calcium ion levels and enhancing MAPK1/MAPK3 activation. Acts as a receptor for extracellular ubiquitin; leading to enhanced intracellular calcium ions and reduced cellular cAMP levels. Involved in hematopoiesis and in cardiac ventricular septum formation. Also plays an essential role in vascularization of the gastrointestinal tract, probably by regulating vascular branching and/or remodeling processes in endothelial cells. Involved in cerebellar development. In the CNS, could mediate hippocampal-neuron survival. Acts as a coreceptor (CD4 being the primary receptor) for HIV-1 X4 isolates and as a primary receptor for some HIV-2 isolates. Promotes Env-mediated fusion of the virus.<ref>PMID:8329116</ref> <ref>PMID:8234909</ref> <ref>PMID:8629022</ref> <ref>PMID:8752280</ref> <ref>PMID:8752281</ref> <ref>PMID:10074102</ref> <ref>PMID:10644702</ref> <ref>PMID:10825158</ref> <ref>PMID:17197449</ref> <ref>PMID:20048153</ref> <ref>PMID:20228059</ref> <ref>PMID:20505072</ref> <br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Synthetic construct]]<br />
[[Category: Baker D]]<br />
[[Category: Banerjee N]]<br />
[[Category: Banerjee R]]<br />
[[Category: Ganguly M]]<br />
[[Category: Muratspahic E]]<br />
[[Category: Shukla AK]]<br />
[[Category: Tiwari D]]</div>OCAhttps://proteopedia.org/index.php?title=1sqn&diff=44901211sqn2026-09-09T08:15:24Z<p>OCA: </p>
<hr />
<div><br />
==Progesterone Receptor Ligand Binding Domain with bound Norethindrone==<br />
<StructureSection load='1sqn' size='340' side='right'caption='[[1sqn]], [[Resolution|resolution]] 1.45&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[1sqn]] 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=1SQN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SQN FirstGlance]. <br><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]] 1.451&#8491;</td></tr><br />
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDR:(14BETA,17ALPHA)-17-ETHYNYL-17-HYDROXYESTR-4-EN-3-ONE'>NDR</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1sqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1sqn OCA], [https://pdbe.org/1sqn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1sqn RCSB], [https://www.ebi.ac.uk/pdbsum/1sqn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1sqn ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[https://www.uniprot.org/uniprot/PRGR_HUMAN PRGR_HUMAN] The steroid hormones and their receptors are involved in the regulation of eukaryotic gene expression and affect cellular proliferation and differentiation in target tissues. Progesterone receptor isoform B (PRB) is involved activation of c-SRC/MAPK signaling on hormone stimulation.<ref>PMID:15572662</ref> <ref>PMID:15798179</ref> <ref>PMID:17020914</ref> <ref>PMID:17347654</ref> <ref>PMID:17717077</ref> <ref>PMID:17173941</ref> <ref>PMID:18202149</ref> Isoform A is inactive in stimulating c-Src/MAPK signaling on hormone stimulation.<ref>PMID:15572662</ref> <ref>PMID:15798179</ref> <ref>PMID:17020914</ref> <ref>PMID:17347654</ref> <ref>PMID:17717077</ref> <ref>PMID:17173941</ref> <ref>PMID:18202149</ref> <br />
== Evolutionary Conservation ==<br />
[[Image:Consurf_key_small.gif|200px|right]]<br />
Check<jmol><br />
<jmolCheckbox><br />
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sq/1sqn_consurf.spt"</scriptWhenChecked><br />
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked><br />
<text>to colour the structure by Evolutionary Conservation</text><br />
</jmolCheckbox><br />
</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=1sqn ConSurf].<br />
<div style="clear:both"></div><br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
Although progesterone, the natural ligand of the progesterone receptor (PR), has a hydrogen atom at the 17alpha position, other potent steroid agonists such as norethindrone and mometasone furoate have larger substituents at this position that are accommodated by the PR ligand binding pocket. Crystallographic analysis of PR ligand binding domain complexes clearly demonstrated that these moieties were accommodated by local shifts of the protein main chain and by adoption of alternative side chain rotamer conformations of ligand-proximal amino acids. These conformational changes imparted a ligand-specific volume to the binding pocket, from 490 A3 in the metribolone complex to 520 A3 in the norethindrone complex, 565 A3 in the progesterone complex, and 730 A3 in the mometasone furoate complex. Despite these marked alterations in binding pocket volume, critical interactions essential for establishment of an active AF2 conformation were maintained.<br />
<br />
Progesterone receptor ligand binding pocket flexibility: crystal structures of the norethindrone and mometasone furoate complexes.,Madauss KP, Deng SJ, Austin RJ, Lambert MH, McLay I, Pritchard J, Short SA, Stewart EL, Uings IJ, Williams SP J Med Chem. 2004 Jun 17;47(13):3381-7. PMID:15189034<ref>PMID:15189034</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 1sqn" style="background-color:#fffaf0;"></div><br />
<br />
==See Also==<br />
*[[Progesterone receptor|Progesterone receptor]]<br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Austin RJH]]<br />
[[Category: Deng J-S]]<br />
[[Category: Lambert MH]]<br />
[[Category: Madauss KP]]<br />
[[Category: McLay I]]<br />
[[Category: Pritchard J]]<br />
[[Category: Short SA]]<br />
[[Category: Stewart EL]]<br />
[[Category: Uings IJ]]<br />
[[Category: Williams SP]]</div>OCAhttps://proteopedia.org/index.php?title=Category:Sundberg_B&diff=4490120Category:Sundberg B2026-09-09T08:14:17Z<p>OCA: Protected "Category:Sundberg B": Seeded page ([Edit=Allow only administrators] (indefinite) [Move=Allow only administrators] (indefinite))</p>
<hr />
<div>List of pages with the keyword Sundberg B</div>OCAhttps://proteopedia.org/index.php?title=Category:Sundberg_B&diff=4490119Category:Sundberg B2026-09-09T08:14:16Z<p>OCA: Created page with "List of pages with the keyword Sundberg B"</p>
<hr />
<div>List of pages with the keyword Sundberg B</div>OCAhttps://proteopedia.org/index.php?title=10oj&diff=449011810oj2026-09-09T08:14:11Z<p>OCA: </p>
<hr />
<div><br />
==The crystal structure of apo phosphofructokinase from Escherichia coli==<br />
<StructureSection load='10oj' size='340' side='right'caption='[[10oj]], [[Resolution|resolution]] 2.60&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[10oj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=10OJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=10OJ FirstGlance]. <br><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]] 2.6&#8491;</td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=10oj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=10oj OCA], [https://pdbe.org/10oj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=10oj RCSB], [https://www.ebi.ac.uk/pdbsum/10oj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=10oj ProSAT]</span></td></tr><br />
</table><br />
__TOC__<br />
</StructureSection><br />
[[Category: Escherichia coli]]<br />
[[Category: Large Structures]]<br />
[[Category: Glasgow A]]<br />
[[Category: Gong Z]]<br />
[[Category: Lu C]]<br />
[[Category: Sundberg B]]<br />
[[Category: Weber KC]]<br />
[[Category: Wells ML]]</div>OCAhttps://proteopedia.org/index.php?title=9zvx&diff=44901179zvx2026-09-09T08:14:03Z<p>OCA: </p>
<hr />
<div><br />
==Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryoEM==<br />
<StructureSection load='9zvx' size='340' side='right'caption='[[9zvx]], [[Resolution|resolution]] 3.40&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[9zvx]] is a 4 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=9ZVX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9ZVX FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.4&#8491;</td></tr><br />
<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=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9zvx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9zvx OCA], [https://pdbe.org/9zvx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9zvx RCSB], [https://www.ebi.ac.uk/pdbsum/9zvx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9zvx ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[https://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN] Defects in F11 are the cause of factor XI deficiency (FA11D) [MIM:[https://omim.org/entry/612416 612416]; also known as plasma thromboplastin antecedent deficiency or Rosenthal syndrome. It is a hemorrhagic disease characterized by reduced levels and activity of factor XI resulting in moderate bleeding symptoms, usually occurring after trauma or surgery. Patients usually do not present spontaneous bleeding but women can present with menorrhagia. Hemorrhages are usually moderate.<ref>PMID:2813350</ref> <ref>PMID:1547342</ref> <ref>PMID:7888672</ref> <ref>PMID:7669672</ref> <ref>PMID:9401068</ref> <ref>PMID:9787168</ref> <ref>PMID:10027710</ref> <ref>PMID:10606881</ref> <ref>PMID:11895778</ref> <ref>PMID:15026311</ref> <ref>PMID:15180874</ref> <ref>PMID:15953011</ref> <ref>PMID:16607084</ref> <ref>PMID:18005151</ref> <ref>PMID:21668437</ref> <ref>PMID:21457405</ref> <ref>PMID:22016685</ref> <ref>PMID:22322133</ref> <ref>PMID:21999818</ref> <ref>PMID:22159456</ref> <br />
== Function ==<br />
[https://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN] Factor XI triggers the middle phase of the intrinsic pathway of blood coagulation by activating factor IX.<br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
BACKGROUND: Factor XI (FXI) occupies a unique and clinically significant niche, bridging the tissue factor-driven and contact-driven coagulation pathways. Irrespective of the trigger, activated factor XI (FXIa) contributes to clotting by activating factor IX (FIX). Biochemical studies established that this reaction requires the membrane-binding FIX-Gla domain to engage an exosite on the FXIa Apple 3 (A3) domain, that only become available upon FXI activation. Structural data for FXIa, FIX, FIXabeta, and the FXIa:FIX complex are lacking; current understanding relies on zymogen FXI crystal structures and homology modeling of FXIa after kallikrein. OBJECTIVES: Elucidate the high-resolution structure of FXIa in functionally relevant conformation in complex with FIX. METHODS: We utilized cryogenic electron microscopy (cryo-EM) to determine the structures of human FXIa in complex with its full-length substrate, FIX, and activated product, FIXabeta. RESULTS: We report the first cryo-EM structures of FXIa in complex with its substrate, FIX, and activated FIX (FIXabeta). The structures capture a functionally relevant conformational change in the FXIa catalytic domain and reveals the first view of the entire FIX and FIXabeta. Critically, we visualize the FIX-Gla domain precisely docked to the FXIa-A3 exosite on both subunits of the FXIa dimer. We also define the first step of proteolysis, visualizing the FIX Arg145 inserted into the primary specificity pocket of FXIa. CONCLUSIONS: The structures define the full FXIa:FIX interface providing a structural template for understanding the sequential activation of FIX and for developing a new class of selective allosteric antithrombotic agents.<br />
<br />
Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryo-EM.,Mohammed BM, Deavila S, Friet T, Dattilio I J Thromb Haemost. 2026 Aug 21:S1538-7836(26)00539-8. doi: , 10.1016/j.jtha.2026.08.015. PMID:42628751<ref>PMID:42628751</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 9zvx" style="background-color:#fffaf0;"></div><br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Mohammed BM]]</div>OCAhttps://proteopedia.org/index.php?title=9zun&diff=44901169zun2026-09-09T08:14:02Z<p>OCA: </p>
<hr />
<div><br />
==Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryoEM==<br />
<StructureSection load='9zun' size='340' side='right'caption='[[9zun]], [[Resolution|resolution]] 3.55&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[9zun]] is a 3 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=9ZUN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9ZUN FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.55&#8491;</td></tr><br />
<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=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9zun FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9zun OCA], [https://pdbe.org/9zun PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9zun RCSB], [https://www.ebi.ac.uk/pdbsum/9zun PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9zun ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[https://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN] Defects in F11 are the cause of factor XI deficiency (FA11D) [MIM:[https://omim.org/entry/612416 612416]; also known as plasma thromboplastin antecedent deficiency or Rosenthal syndrome. It is a hemorrhagic disease characterized by reduced levels and activity of factor XI resulting in moderate bleeding symptoms, usually occurring after trauma or surgery. Patients usually do not present spontaneous bleeding but women can present with menorrhagia. Hemorrhages are usually moderate.<ref>PMID:2813350</ref> <ref>PMID:1547342</ref> <ref>PMID:7888672</ref> <ref>PMID:7669672</ref> <ref>PMID:9401068</ref> <ref>PMID:9787168</ref> <ref>PMID:10027710</ref> <ref>PMID:10606881</ref> <ref>PMID:11895778</ref> <ref>PMID:15026311</ref> <ref>PMID:15180874</ref> <ref>PMID:15953011</ref> <ref>PMID:16607084</ref> <ref>PMID:18005151</ref> <ref>PMID:21668437</ref> <ref>PMID:21457405</ref> <ref>PMID:22016685</ref> <ref>PMID:22322133</ref> <ref>PMID:21999818</ref> <ref>PMID:22159456</ref> <br />
== Function ==<br />
[https://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN] Factor XI triggers the middle phase of the intrinsic pathway of blood coagulation by activating factor IX.<br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
BACKGROUND: Factor XI (FXI) occupies a unique and clinically significant niche, bridging the tissue factor-driven and contact-driven coagulation pathways. Irrespective of the trigger, activated factor XI (FXIa) contributes to clotting by activating factor IX (FIX). Biochemical studies established that this reaction requires the membrane-binding FIX-Gla domain to engage an exosite on the FXIa Apple 3 (A3) domain, that only become available upon FXI activation. Structural data for FXIa, FIX, FIXabeta, and the FXIa:FIX complex are lacking; current understanding relies on zymogen FXI crystal structures and homology modeling of FXIa after kallikrein. OBJECTIVES: Elucidate the high-resolution structure of FXIa in functionally relevant conformation in complex with FIX. METHODS: We utilized cryogenic electron microscopy (cryo-EM) to determine the structures of human FXIa in complex with its full-length substrate, FIX, and activated product, FIXabeta. RESULTS: We report the first cryo-EM structures of FXIa in complex with its substrate, FIX, and activated FIX (FIXabeta). The structures capture a functionally relevant conformational change in the FXIa catalytic domain and reveals the first view of the entire FIX and FIXabeta. Critically, we visualize the FIX-Gla domain precisely docked to the FXIa-A3 exosite on both subunits of the FXIa dimer. We also define the first step of proteolysis, visualizing the FIX Arg145 inserted into the primary specificity pocket of FXIa. CONCLUSIONS: The structures define the full FXIa:FIX interface providing a structural template for understanding the sequential activation of FIX and for developing a new class of selective allosteric antithrombotic agents.<br />
<br />
Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryo-EM.,Mohammed BM, Deavila S, Friet T, Dattilio I J Thromb Haemost. 2026 Aug 21:S1538-7836(26)00539-8. doi: , 10.1016/j.jtha.2026.08.015. PMID:42628751<ref>PMID:42628751</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 9zun" style="background-color:#fffaf0;"></div><br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Mohammed BM]]</div>OCAhttps://proteopedia.org/index.php?title=9zub&diff=44901159zub2026-09-09T08:13:57Z<p>OCA: </p>
<hr />
<div><br />
==Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryoEM==<br />
<StructureSection load='9zub' size='340' side='right'caption='[[9zub]], [[Resolution|resolution]] 3.65&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[9zub]] is a 3 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=9ZUB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9ZUB FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.65&#8491;</td></tr><br />
<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=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9zub FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9zub OCA], [https://pdbe.org/9zub PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9zub RCSB], [https://www.ebi.ac.uk/pdbsum/9zub PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9zub ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[https://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN] Defects in F11 are the cause of factor XI deficiency (FA11D) [MIM:[https://omim.org/entry/612416 612416]; also known as plasma thromboplastin antecedent deficiency or Rosenthal syndrome. It is a hemorrhagic disease characterized by reduced levels and activity of factor XI resulting in moderate bleeding symptoms, usually occurring after trauma or surgery. Patients usually do not present spontaneous bleeding but women can present with menorrhagia. Hemorrhages are usually moderate.<ref>PMID:2813350</ref> <ref>PMID:1547342</ref> <ref>PMID:7888672</ref> <ref>PMID:7669672</ref> <ref>PMID:9401068</ref> <ref>PMID:9787168</ref> <ref>PMID:10027710</ref> <ref>PMID:10606881</ref> <ref>PMID:11895778</ref> <ref>PMID:15026311</ref> <ref>PMID:15180874</ref> <ref>PMID:15953011</ref> <ref>PMID:16607084</ref> <ref>PMID:18005151</ref> <ref>PMID:21668437</ref> <ref>PMID:21457405</ref> <ref>PMID:22016685</ref> <ref>PMID:22322133</ref> <ref>PMID:21999818</ref> <ref>PMID:22159456</ref> <br />
== Function ==<br />
[https://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN] Factor XI triggers the middle phase of the intrinsic pathway of blood coagulation by activating factor IX.<br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
BACKGROUND: Factor XI (FXI) occupies a unique and clinically significant niche, bridging the tissue factor-driven and contact-driven coagulation pathways. Irrespective of the trigger, activated factor XI (FXIa) contributes to clotting by activating factor IX (FIX). Biochemical studies established that this reaction requires the membrane-binding FIX-Gla domain to engage an exosite on the FXIa Apple 3 (A3) domain, that only become available upon FXI activation. Structural data for FXIa, FIX, FIXabeta, and the FXIa:FIX complex are lacking; current understanding relies on zymogen FXI crystal structures and homology modeling of FXIa after kallikrein. OBJECTIVES: Elucidate the high-resolution structure of FXIa in functionally relevant conformation in complex with FIX. METHODS: We utilized cryogenic electron microscopy (cryo-EM) to determine the structures of human FXIa in complex with its full-length substrate, FIX, and activated product, FIXabeta. RESULTS: We report the first cryo-EM structures of FXIa in complex with its substrate, FIX, and activated FIX (FIXabeta). The structures capture a functionally relevant conformational change in the FXIa catalytic domain and reveals the first view of the entire FIX and FIXabeta. Critically, we visualize the FIX-Gla domain precisely docked to the FXIa-A3 exosite on both subunits of the FXIa dimer. We also define the first step of proteolysis, visualizing the FIX Arg145 inserted into the primary specificity pocket of FXIa. CONCLUSIONS: The structures define the full FXIa:FIX interface providing a structural template for understanding the sequential activation of FIX and for developing a new class of selective allosteric antithrombotic agents.<br />
<br />
Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryo-EM.,Mohammed BM, Deavila S, Friet T, Dattilio I J Thromb Haemost. 2026 Aug 21:S1538-7836(26)00539-8. doi: , 10.1016/j.jtha.2026.08.015. PMID:42628751<ref>PMID:42628751</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 9zub" style="background-color:#fffaf0;"></div><br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Mohammed BM]]</div>OCAhttps://proteopedia.org/index.php?title=9ztk&diff=44901149ztk2026-09-09T08:13:55Z<p>OCA: </p>
<hr />
<div><br />
==Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryoEM==<br />
<StructureSection load='9ztk' size='340' side='right'caption='[[9ztk]], [[Resolution|resolution]] 3.70&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[9ztk]] is a 3 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=9ZTK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9ZTK FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.7&#8491;</td></tr><br />
<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=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9ztk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9ztk OCA], [https://pdbe.org/9ztk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9ztk RCSB], [https://www.ebi.ac.uk/pdbsum/9ztk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9ztk ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[https://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN] Defects in F11 are the cause of factor XI deficiency (FA11D) [MIM:[https://omim.org/entry/612416 612416]; also known as plasma thromboplastin antecedent deficiency or Rosenthal syndrome. It is a hemorrhagic disease characterized by reduced levels and activity of factor XI resulting in moderate bleeding symptoms, usually occurring after trauma or surgery. Patients usually do not present spontaneous bleeding but women can present with menorrhagia. Hemorrhages are usually moderate.<ref>PMID:2813350</ref> <ref>PMID:1547342</ref> <ref>PMID:7888672</ref> <ref>PMID:7669672</ref> <ref>PMID:9401068</ref> <ref>PMID:9787168</ref> <ref>PMID:10027710</ref> <ref>PMID:10606881</ref> <ref>PMID:11895778</ref> <ref>PMID:15026311</ref> <ref>PMID:15180874</ref> <ref>PMID:15953011</ref> <ref>PMID:16607084</ref> <ref>PMID:18005151</ref> <ref>PMID:21668437</ref> <ref>PMID:21457405</ref> <ref>PMID:22016685</ref> <ref>PMID:22322133</ref> <ref>PMID:21999818</ref> <ref>PMID:22159456</ref> <br />
== Function ==<br />
[https://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN] Factor XI triggers the middle phase of the intrinsic pathway of blood coagulation by activating factor IX.<br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
BACKGROUND: Factor XI (FXI) occupies a unique and clinically significant niche, bridging the tissue factor-driven and contact-driven coagulation pathways. Irrespective of the trigger, activated factor XI (FXIa) contributes to clotting by activating factor IX (FIX). Biochemical studies established that this reaction requires the membrane-binding FIX-Gla domain to engage an exosite on the FXIa Apple 3 (A3) domain, that only become available upon FXI activation. Structural data for FXIa, FIX, FIXabeta, and the FXIa:FIX complex are lacking; current understanding relies on zymogen FXI crystal structures and homology modeling of FXIa after kallikrein. OBJECTIVES: Elucidate the high-resolution structure of FXIa in functionally relevant conformation in complex with FIX. METHODS: We utilized cryogenic electron microscopy (cryo-EM) to determine the structures of human FXIa in complex with its full-length substrate, FIX, and activated product, FIXabeta. RESULTS: We report the first cryo-EM structures of FXIa in complex with its substrate, FIX, and activated FIX (FIXabeta). The structures capture a functionally relevant conformational change in the FXIa catalytic domain and reveals the first view of the entire FIX and FIXabeta. Critically, we visualize the FIX-Gla domain precisely docked to the FXIa-A3 exosite on both subunits of the FXIa dimer. We also define the first step of proteolysis, visualizing the FIX Arg145 inserted into the primary specificity pocket of FXIa. CONCLUSIONS: The structures define the full FXIa:FIX interface providing a structural template for understanding the sequential activation of FIX and for developing a new class of selective allosteric antithrombotic agents.<br />
<br />
Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryo-EM.,Mohammed BM, Deavila S, Friet T, Dattilio I J Thromb Haemost. 2026 Aug 21:S1538-7836(26)00539-8. doi: , 10.1016/j.jtha.2026.08.015. PMID:42628751<ref>PMID:42628751</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 9ztk" style="background-color:#fffaf0;"></div><br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Mohammed BM]]</div>OCAhttps://proteopedia.org/index.php?title=9zqy&diff=44901139zqy2026-09-09T08:13:52Z<p>OCA: </p>
<hr />
<div><br />
==Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryoEM==<br />
<StructureSection load='9zqy' size='340' side='right'caption='[[9zqy]], [[Resolution|resolution]] 3.09&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[9zqy]] is a 6 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=9ZQY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9ZQY FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.09&#8491;</td></tr><br />
<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=CGU:GAMMA-CARBOXY-GLUTAMIC+ACID'>CGU</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9zqy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9zqy OCA], [https://pdbe.org/9zqy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9zqy RCSB], [https://www.ebi.ac.uk/pdbsum/9zqy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9zqy ProSAT]</span></td></tr><br />
</table><br />
== Disease ==<br />
[https://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN] Defects in F11 are the cause of factor XI deficiency (FA11D) [MIM:[https://omim.org/entry/612416 612416]; also known as plasma thromboplastin antecedent deficiency or Rosenthal syndrome. It is a hemorrhagic disease characterized by reduced levels and activity of factor XI resulting in moderate bleeding symptoms, usually occurring after trauma or surgery. Patients usually do not present spontaneous bleeding but women can present with menorrhagia. Hemorrhages are usually moderate.<ref>PMID:2813350</ref> <ref>PMID:1547342</ref> <ref>PMID:7888672</ref> <ref>PMID:7669672</ref> <ref>PMID:9401068</ref> <ref>PMID:9787168</ref> <ref>PMID:10027710</ref> <ref>PMID:10606881</ref> <ref>PMID:11895778</ref> <ref>PMID:15026311</ref> <ref>PMID:15180874</ref> <ref>PMID:15953011</ref> <ref>PMID:16607084</ref> <ref>PMID:18005151</ref> <ref>PMID:21668437</ref> <ref>PMID:21457405</ref> <ref>PMID:22016685</ref> <ref>PMID:22322133</ref> <ref>PMID:21999818</ref> <ref>PMID:22159456</ref> <br />
== Function ==<br />
[https://www.uniprot.org/uniprot/FA11_HUMAN FA11_HUMAN] Factor XI triggers the middle phase of the intrinsic pathway of blood coagulation by activating factor IX.<br />
<div style="background-color:#fffaf0;"><br />
== Publication Abstract from PubMed ==<br />
BACKGROUND: Factor XI (FXI) occupies a unique and clinically significant niche, bridging the tissue factor-driven and contact-driven coagulation pathways. Irrespective of the trigger, activated factor XI (FXIa) contributes to clotting by activating factor IX (FIX). Biochemical studies established that this reaction requires the membrane-binding FIX-Gla domain to engage an exosite on the FXIa Apple 3 (A3) domain, that only become available upon FXI activation. Structural data for FXIa, FIX, FIXabeta, and the FXIa:FIX complex are lacking; current understanding relies on zymogen FXI crystal structures and homology modeling of FXIa after kallikrein. OBJECTIVES: Elucidate the high-resolution structure of FXIa in functionally relevant conformation in complex with FIX. METHODS: We utilized cryogenic electron microscopy (cryo-EM) to determine the structures of human FXIa in complex with its full-length substrate, FIX, and activated product, FIXabeta. RESULTS: We report the first cryo-EM structures of FXIa in complex with its substrate, FIX, and activated FIX (FIXabeta). The structures capture a functionally relevant conformational change in the FXIa catalytic domain and reveals the first view of the entire FIX and FIXabeta. Critically, we visualize the FIX-Gla domain precisely docked to the FXIa-A3 exosite on both subunits of the FXIa dimer. We also define the first step of proteolysis, visualizing the FIX Arg145 inserted into the primary specificity pocket of FXIa. CONCLUSIONS: The structures define the full FXIa:FIX interface providing a structural template for understanding the sequential activation of FIX and for developing a new class of selective allosteric antithrombotic agents.<br />
<br />
Structural insights into the exosite-mediated activation of Factor IX by Factor XIa using cryo-EM.,Mohammed BM, Deavila S, Friet T, Dattilio I J Thromb Haemost. 2026 Aug 21:S1538-7836(26)00539-8. doi: , 10.1016/j.jtha.2026.08.015. PMID:42628751<ref>PMID:42628751</ref><br />
<br />
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br><br />
</div><br />
<div class="pdbe-citations 9zqy" style="background-color:#fffaf0;"></div><br />
== References ==<br />
<references/><br />
__TOC__<br />
</StructureSection><br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Mohammed BM]]</div>OCAhttps://proteopedia.org/index.php?title=9zbc&diff=44901129zbc2026-09-09T08:13:49Z<p>OCA: </p>
<hr />
<div><br />
==Human GGPPS in the Open Hexamer Conformation==<br />
<StructureSection load='9zbc' size='340' side='right'caption='[[9zbc]], [[Resolution|resolution]] 2.25&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[9zbc]] is a 6 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=9ZBC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9ZBC FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.25&#8491;</td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9zbc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9zbc OCA], [https://pdbe.org/9zbc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9zbc RCSB], [https://www.ebi.ac.uk/pdbsum/9zbc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9zbc ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[https://www.uniprot.org/uniprot/GGPPS_HUMAN GGPPS_HUMAN] Catalyzes the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate, an important precursor of carotenoids and geranylated proteins.<br />
__TOC__<br />
</StructureSection><br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Ferens FG]]<br />
[[Category: Lemieux MJ]]<br />
[[Category: Tsantrizos YS]]</div>OCAhttps://proteopedia.org/index.php?title=9zbd&diff=44901119zbd2026-09-09T08:13:47Z<p>OCA: </p>
<hr />
<div><br />
==Human GGPPS in the Closed Hexamer Conformation==<br />
<StructureSection load='9zbd' size='340' side='right'caption='[[9zbd]], [[Resolution|resolution]] 2.36&Aring;' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>[[9zbd]] is a 6 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=9ZBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9ZBD FirstGlance]. <br><br />
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.36&#8491;</td></tr><br />
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9zbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9zbd OCA], [https://pdbe.org/9zbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9zbd RCSB], [https://www.ebi.ac.uk/pdbsum/9zbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9zbd ProSAT]</span></td></tr><br />
</table><br />
== Function ==<br />
[https://www.uniprot.org/uniprot/GGPPS_HUMAN GGPPS_HUMAN] Catalyzes the trans-addition of the three molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate, an important precursor of carotenoids and geranylated proteins.<br />
__TOC__<br />
</StructureSection><br />
[[Category: Homo sapiens]]<br />
[[Category: Large Structures]]<br />
[[Category: Ferens FG]]<br />
[[Category: Lemieux MJ]]<br />
[[Category: Tsantrizos YS]]</div>OCAhttps://proteopedia.org/index.php?title=9zbb&diff=44901109zbb2026-09-09T08:13:44Z<p>OCA: </p>
<hr />
<div><br />
====<br />
<StructureSection load='9zbb' size='340' side='right'caption='[[9zbb]]' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br><br />
</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=9zbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9zbb OCA], [https://pdbe.org/9zbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9zbb RCSB], [https://www.ebi.ac.uk/pdbsum/9zbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9zbb ProSAT]</span></td></tr><br />
</table><br />
__TOC__<br />
</StructureSection><br />
[[Category: Large Structures]]<br />
[[Category: Z-disk]]</div>OCAhttps://proteopedia.org/index.php?title=9zba&diff=44901099zba2026-09-09T08:13:41Z<p>OCA: </p>
<hr />
<div><br />
====<br />
<StructureSection load='9zba' size='340' side='right'caption='[[9zba]]' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br><br />
</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=9zba FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9zba OCA], [https://pdbe.org/9zba PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9zba RCSB], [https://www.ebi.ac.uk/pdbsum/9zba PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9zba ProSAT]</span></td></tr><br />
</table><br />
__TOC__<br />
</StructureSection><br />
[[Category: Large Structures]]<br />
[[Category: Z-disk]]</div>OCAhttps://proteopedia.org/index.php?title=9zb9&diff=44901089zb92026-09-09T08:13:41Z<p>OCA: </p>
<hr />
<div><br />
====<br />
<StructureSection load='9zb9' size='340' side='right'caption='[[9zb9]]' scene=''><br />
== Structural highlights ==<br />
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br><br />
</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=9zb9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9zb9 OCA], [https://pdbe.org/9zb9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9zb9 RCSB], [https://www.ebi.ac.uk/pdbsum/9zb9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9zb9 ProSAT]</span></td></tr><br />
</table><br />
__TOC__<br />
</StructureSection><br />
[[Category: Large Structures]]<br />
[[Category: Z-disk]]</div>OCA