5ifj - Revision history

OCA at 13:49, 30 August 2023

2023-08-30T13:49:31Z

←Older revision		Revision as of 13:49, 30 August 2023
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	<StructureSection load='5ifj' size='340' side='right'caption='[[5ifj]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='5ifj' size='340' side='right'caption='[[5ifj]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ifj]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5IFJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ifj]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Triticum_aestivum Triticum aestivum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5IFJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.35Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5ifj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifj OCA], [~~http~~://pdbe.org/5ifj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ifj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ifj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifj ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5ifj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifj OCA], [https://pdbe.org/5ifj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ifj RCSB], [https://www.ebi.ac.uk/pdbsum/5ifj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifj ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 23:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Chen, X~~]]	+	[[Category: Triticum aestivum]]
-	[[Category: ~~Gidoni, M~~]]	+	[[Category: Chen X]]
-	[[Category: ~~Lundin, K E~~]]	+	[[Category: Gidoni M]]
-	[[Category: ~~Pre, M F.du~~]]	+	[[Category: Lundin KE]]
-	[[Category: Snir, O]]	+	[[Category: Snir O]]
-	[[Category: Sollid~~, L M~~]]	+	[[Category: Sollid LM]]
-	[[Category: Steinsbo, O]]	+	[[Category: Steinsbo O]]
-	[[Category: Yaari, G]]	+	[[Category: Yaari G]]
-	[[Category: Zhao, Y]]	+	[[Category: Zhao Y]]
-	[[Category: ~~Anti-gliadin antibody]]~~	+	[[Category: Du Pre MF]]
-	~~[[Category: Celiac disease]]~~	+
-	~~[[Category: Gliadin peptide]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 07:16, 3 June 2020

2020-06-03T07:16:45Z

←Older revision		Revision as of 07:16, 3 June 2020
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	==Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide PLQPEQPFP==		==Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide PLQPEQPFP==
-	<StructureSection load='5ifj' size='340' side='right' caption='[[5ifj]], [[Resolution\|resolution]] 2.35Å' scene=''>	+	<StructureSection load='5ifj' size='340' side='right'caption='[[5ifj]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ifj]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFJ OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5IFJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ifj]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5IFJ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ifj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifj OCA], [http://pdbe.org/5ifj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ifj RCSB], [http://www.ebi.ac.uk/pdbsum/5ifj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifj ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5ifj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifj OCA], [http://pdbe.org/5ifj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ifj RCSB], [http://www.ebi.ac.uk/pdbsum/5ifj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifj ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 5ifj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ifj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Albumin 3D structures\|Albumin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 21:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Chen, X]]		[[Category: Chen, X]]
	[[Category: Gidoni, M]]		[[Category: Gidoni, M]]

OCA at 07:36, 6 December 2017

2017-12-06T07:36:01Z

←Older revision		Revision as of 07:36, 6 December 2017
Line 3:		Line 3:
	<StructureSection load='5ifj' size='340' side='right' caption='[[5ifj]], [[Resolution\|resolution]] 2.35Å' scene=''>		<StructureSection load='5ifj' size='340' side='right' caption='[[5ifj]], [[Resolution\|resolution]] 2.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ifj]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IFJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ifj]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IFJ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ifj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifj OCA], [http://pdbe.org/5ifj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ifj RCSB], [http://www.ebi.ac.uk/pdbsum/5ifj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifj ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ifj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifj OCA], [http://pdbe.org/5ifj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ifj RCSB], [http://www.ebi.ac.uk/pdbsum/5ifj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifj ProSAT]</span></td></tr>
Line 16:		Line 16:
	</div>		</div>
	<div class="pdbe-citations 5ifj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ifj" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Albumin\|Albumin]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Chen, X]]		[[Category: Chen, X]]
-	[[Category: ~~Harlos~~, K]]	+	[[Category: Gidoni, M]]
		+	[[Category: Lundin, K E]]
		+	[[Category: Pre, M F.du]]
	[[Category: Snir, O]]		[[Category: Snir, O]]
	[[Category: Sollid, L M]]		[[Category: Sollid, L M]]
		+	[[Category: Steinsbo, O]]
		+	[[Category: Yaari, G]]
	[[Category: Zhao, Y]]		[[Category: Zhao, Y]]
	[[Category: Anti-gliadin antibody]]		[[Category: Anti-gliadin antibody]]

OCA at 09:23, 4 October 2017

2017-10-04T09:23:07Z

←Older revision		Revision as of 09:23, 4 October 2017
Line 7:		Line 7:
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ifj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifj OCA], [http://pdbe.org/5ifj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ifj RCSB], [http://www.ebi.ac.uk/pdbsum/5ifj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifj ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ifj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifj OCA], [http://pdbe.org/5ifj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ifj RCSB], [http://www.ebi.ac.uk/pdbsum/5ifj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifj ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The role of B cells and posttranslational modifications in pathogenesis of organ-specific immune diseases is increasingly envisioned but remains poorly understood, particularly in human disorders. In celiac disease, transglutaminase 2-modified (TG2-modified; deamidated) gluten peptides drive disease-specific T cell and B cell responses, and antibodies to deamidated gluten peptides are excellent diagnostic markers. Here, we substantiate by high-throughput sequencing of IGHV genes that antibodies to a disease-specific, deamidated, and immunodominant B cell epitope of gluten (PLQPEQPFP) have biased and stereotyped usage of IGHV3-23 and IGHV3-15 gene segments with modest somatic mutations. X-ray crystal structures of 2 prototype IGHV3-15/IGKV4-1 and IGHV3-23/IGLV4-69 antibodies reveal peptide interaction mainly via germline-encoded residues. In-depth mutational analysis showed restricted selection and substitution patterns at positions involved in antigen binding. While the IGHV3-15/IGKV4-1 antibody interacts with Glu5 and Gln6, the IGHV3-23/IGLV4-69 antibody interacts with Gln3, Pro4, Pro7, and Phe8 - residues involved in substrate recognition by TG2. Hence, both antibodies, despite different interaction with the epitope, recognize signatures of TG2 processing that facilitates B cell presentation of deamidated gluten peptides to T cells, thereby providing a molecular framework for the generation of these clinically important antibodies. The study provides essential insight into the pathogenic mechanism of celiac disease.
		+
		+	Stereotyped antibody responses target posttranslationally modified gluten in celiac disease.,Snir O, Chen X, Gidoni M, du Pre MF, Zhao Y, Steinsbo O, Lundin KE, Yaari G, Sollid LM JCI Insight. 2017 Sep 7;2(17). pii: 93961. doi: 10.1172/jci.insight.93961. PMID:28878138<ref>PMID:28878138</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5ifj" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Albumin\|Albumin]]		*[[Albumin\|Albumin]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 21:17, 15 March 2017

2017-03-15T21:17:29Z

←Older revision		Revision as of 21:17, 15 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5ifj is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide PLQPEQPFP==
		+	<StructureSection load='5ifj' size='340' side='right' caption='[[5ifj]], [[Resolution\|resolution]] 2.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ifj]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5IFJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5IFJ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ifj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ifj OCA], [http://pdbe.org/5ifj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ifj RCSB], [http://www.ebi.ac.uk/pdbsum/5ifj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ifj ProSAT]</span></td></tr>
		+	</table>

-	~~Authors: Chen, X., Zhao, Y., Harlos, K., Snir, O., Sollid, L.M.~~	+	==See Also==
-		+	*[[Albumin\|Albumin]]
-	~~Description: Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide PLQPEQPFP~~	+	__TOC__
-	[[~~Category: Unreleased Structures~~]]	+	</StructureSection>
-	~~[[Category: Snir, O]]~~	+
-	~~[[Category: Sollid, L.M]]~~	+
	[[Category: Chen, X]]		[[Category: Chen, X]]
	[[Category: Harlos, K]]		[[Category: Harlos, K]]
		+	[[Category: Snir, O]]
		+	[[Category: Sollid, L M]]
	[[Category: Zhao, Y]]		[[Category: Zhao, Y]]
		+	[[Category: Anti-gliadin antibody]]
		+	[[Category: Celiac disease]]
		+	[[Category: Gliadin peptide]]
		+	[[Category: Immune system]]

OCA at 09:34, 9 March 2017

2017-03-09T09:34:12Z

←Older revision		Revision as of 09:34, 9 March 2017
Line 5:		Line 5:
	Authors: Chen, X., Zhao, Y., Harlos, K., Snir, O., Sollid, L.M.		Authors: Chen, X., Zhao, Y., Harlos, K., Snir, O., Sollid, L.M.

-	Description: Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex ~~ofpeptide~~ PLQPEQPFP	+	Description: Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide PLQPEQPFP
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Snir, O]]		[[Category: Snir, O]]

OCA at 00:27, 11 May 2016

2016-05-11T00:27:33Z

←Older revision		Revision as of 00:27, 11 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5ifj is ON HOLD	+	The entry 5ifj is ON HOLD until Paper Publication

-	Authors: Xi Chen, ~~Yuguang~~ Zhao	+	Authors: Chen, X., Zhao, Y., Harlos, K., Snir, O., Sollid, L.M.

-	Description: Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex ~~of peptide~~ PLQPEQPFP	+	Description: Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex ofpeptide PLQPEQPFP
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Xi Chen, ~~Yuguang~~ Zhao]]	+	[[Category: Snir, O]]
		+	[[Category: Sollid, L.M]]
		+	[[Category: Chen, X]]
		+	[[Category: Harlos, K]]
		+	[[Category: Zhao, Y]]

OCA: Protected "5ifj" [edit=sysop:move=sysop]

2016-03-02T13:54:04Z

Protected "5ifj" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:54, 2 March 2016

OCA: New page: '''Unreleased structure''' The entry 5ifj is ON HOLD Authors: Xi Chen, Yuguang Zhao Description: Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide PLQPEQPF...

2016-03-02T13:54:03Z

New page: '''Unreleased structure''' The entry 5ifj is ON HOLD Authors: Xi Chen, Yuguang Zhao Description: Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide PLQPEQPF...

New page

'''Unreleased structure'''

The entry 5ifj is ON HOLD

Authors: Xi Chen, Yuguang Zhao

Description: Crystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide PLQPEQPFP
[[Category: Unreleased Structures]]
[[Category: Xi Chen, Yuguang Zhao]]