7jny - Revision history

OCA at 15:07, 18 October 2023

2023-10-18T15:07:31Z

←Older revision		Revision as of 15:07, 18 October 2023
Line 3:		Line 3:
	<StructureSection load='7jny' size='340' side='right'caption='[[7jny]], [[Resolution\|resolution]] 1.88Å' scene=''>		<StructureSection load='7jny' size='340' side='right'caption='[[7jny]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7jny]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4zai 4zai]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JNY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7JNY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7jny]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4zai 4zai]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JNY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JNY FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[4zai\|4zai]]</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]] 1.88Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">CXCL13, BCA1, BLC, SCYB13 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=9606 HUMAN])~~</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=7jny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jny OCA], [https://pdbe.org/7jny PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jny RCSB], [https://www.ebi.ac.uk/pdbsum/7jny PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jny 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=7jny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jny OCA], [~~http~~://pdbe.org/7jny PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7jny RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7jny PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7jny ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CXL13_HUMAN CXL13_HUMAN]] Chemotactic for B-lymphocytes but not for T-lymphocytes, monocytes and neutrophils. Does not induce calcium release in B-lymphocytes. Binds to BLR1/CXCR5.	+	[https://www.uniprot.org/uniprot/CXL13_HUMAN CXL13_HUMAN] Chemotactic for B-lymphocytes but not for T-lymphocytes, monocytes and neutrophils. Does not induce calcium release in B-lymphocytes. Binds to BLR1/CXCR5.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lolis~~, E J~~]]	+	[[Category: Lolis EJ]]
-	[[Category: Murphy~~, J W~~]]	+	[[Category: Murphy JW]]
-	[[Category: Pantouris, G]]	+	[[Category: Pantouris G]]
-	[[Category: Rajasekaran, D]]	+	[[Category: Rajasekaran D]]
-	[[Category: Rosenberg~~, E M]]~~	+	[[Category: Rosenberg Jr EM]]
-	~~[[Category: Chemokine]]~~	+
-	~~[[Category: Cxcl13]]~~	+
-	~~[[Category: Cytokine~~]]	+

OCA at 08:44, 21 October 2020

2020-10-21T08:44:42Z

←Older revision		Revision as of 08:44, 21 October 2020
Line 1:		Line 1:

	==Crystal structure of CXCL13==		==Crystal structure of CXCL13==
-	<StructureSection load='7jny' size='340' side='right'caption='[[7jny]]' scene=''>	+	<StructureSection load='7jny' size='340' side='right'caption='[[7jny]], [[Resolution\|resolution]] 1.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4zai 4zai]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JNY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7JNY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7jny]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4zai 4zai]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JNY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7JNY FirstGlance]. <br>
-	</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=7jny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jny OCA], [http://pdbe.org/7jny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jny RCSB], [http://www.ebi.ac.uk/pdbsum/7jny PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jny ProSAT]</span></td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4zai\|4zai]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CXCL13, BCA1, BLC, SCYB13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=7jny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jny OCA], [http://pdbe.org/7jny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jny RCSB], [http://www.ebi.ac.uk/pdbsum/7jny PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jny ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CXL13_HUMAN CXL13_HUMAN]] Chemotactic for B-lymphocytes but not for T-lymphocytes, monocytes and neutrophils. Does not induce calcium release in B-lymphocytes. Binds to BLR1/CXCR5.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	CXCL13 is the cognate chemokine agonist of CXCR5, a class A G-protein-coupled receptor (GPCR) that is essential for proper humoral immune responses. Using a `methionine scanning' mutagenesis method on the N-terminus of CXCL13, which is the chemokine signaling region, it was shown that minor length alterations and side-chain substitutions still result in CXCR5 activation. This observation indicates that the orthosteric pocket of CXCR5 can tolerate these changes without severely affecting the activity. The introduction of bulk on the ligand was well tolerated by the receptor, whereas a loss of contacts was less tolerated. Furthermore, two crystal structures of CXCL13 mutants were solved, both of which represent the first uncomplexed structures of the human protein. These structures were stabilized by unique interactions formed by the N-termini of the ligands, indicating that CXCL13 exhibits substantial N-terminal flexibility while the chemokine core domain remains largely unchanged. Additionally, it was observed that CXCL13 harbors a large degree of flexibility in the C-terminal extension of the ligand. Comparisons with other published structures of human and murine CXCL13 validate the relative rigidity of the core domain as well as the N- and C-terminal mobilities. Collectively, these mutants and their structures provide the field with additional insights into how CXCL13 interacts with CXCR5.
		+
		+	The N-terminal length and side-chain composition of CXCL13 affect crystallization, structure and functional activity.,Rosenberg EM Jr, Herrington J, Rajasekaran D, Murphy JW, Pantouris G, Lolis EJ Acta Crystallogr D Struct Biol. 2020 Oct 1;76(Pt 10):1033-1049. doi:, 10.1107/S2059798320011687. Epub 2020 Sep 25. PMID:33021505<ref>PMID:33021505</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7jny" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[C-X-C motif chemokine 3D structures\|C-X-C motif chemokine 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lolis EJ]]	+	[[Category: Lolis, E J]]
-	[[Category: Murphy JW]]	+	[[Category: Murphy, J W]]
-	[[Category: Pantouris G]]	+	[[Category: Pantouris, G]]
-	[[Category: Rajasekaran D]]	+	[[Category: Rajasekaran, D]]
-	[[Category: Rosenberg ~~Jr EM~~]]	+	[[Category: Rosenberg, E M]]
		+	[[Category: Chemokine]]
		+	[[Category: Cxcl13]]
		+	[[Category: Cytokine]]

OCA at 06:12, 7 October 2020

2020-10-07T06:12:34Z

←Older revision		Revision as of 06:12, 7 October 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7jny ~~is ON HOLD until Paper Publication~~	+	==Crystal structure of CXCL13==
-		+	<StructureSection load='7jny' size='340' side='right'caption='[[7jny]]' scene=''>
-	~~Authors~~: ~~Rosenberg Jr~~., E.M., ~~Rajasekaran, D~~., ~~Murphy, J~~.W., ~~Pantouris, G~~., ~~Lolis, E~~.J.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4zai 4zai]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JNY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7JNY FirstGlance]. <br>
-	~~Description: Crystal structure of CXCL13~~	+	</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=7jny FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jny OCA], [http://pdbe.org/7jny PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jny RCSB], [http://www.ebi.ac.uk/pdbsum/7jny PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jny ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Pantouris, G~~]]	+	__TOC__
-	[[Category: ~~Lolis, E.J~~]]	+	</StructureSection>
-	[[Category: ~~Rosenberg Jr~~]]	+	[[Category: Large Structures]]
-	[[Category: Rajasekaran, D]]	+	[[Category: Lolis EJ]]
-	[[Category: ~~Murphy, J.W]]~~	+	[[Category: Murphy JW]]
-	~~[[Category: E.M~~]]	+	[[Category: Pantouris G]]
		+	[[Category: Rajasekaran D]]
		+	[[Category: Rosenberg Jr EM]]

OCA at 04:49, 19 August 2020

2020-08-19T04:49:12Z

←Older revision		Revision as of 04:49, 19 August 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7jny is ON HOLD	+	The entry 7jny is ON HOLD until Paper Publication

	Authors: Rosenberg Jr., E.M., Rajasekaran, D., Murphy, J.W., Pantouris, G., Lolis, E.J.		Authors: Rosenberg Jr., E.M., Rajasekaran, D., Murphy, J.W., Pantouris, G., Lolis, E.J.
Line 7:		Line 7:
	Description: Crystal structure of CXCL13		Description: Crystal structure of CXCL13
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
		+	[[Category: Pantouris, G]]
		+	[[Category: Lolis, E.J]]
	[[Category: Rosenberg Jr]]		[[Category: Rosenberg Jr]]
	[[Category: Rajasekaran, D]]		[[Category: Rajasekaran, D]]
-	[[Category: Lolis, E.J]]
-	[[Category: E.M]]
	[[Category: Murphy, J.W]]		[[Category: Murphy, J.W]]
-	[[Category: ~~Pantouris, G~~]]	+	[[Category: E.M]]

OCA: Protected "7jny" [edit=sysop:move=sysop]

2020-08-12T08:33:25Z

Protected "7jny" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:33, 12 August 2020

OCA: New page: '''Unreleased structure''' The entry 7jny is ON HOLD Authors: Rosenberg Jr., E.M., Rajasekaran, D., Murphy, J.W., Pantouris, G., Lolis, E.J. Description: Crystal structure of CXCL13 [[...

2020-08-12T08:33:23Z

New page: '''Unreleased structure''' The entry 7jny is ON HOLD Authors: Rosenberg Jr., E.M., Rajasekaran, D., Murphy, J.W., Pantouris, G., Lolis, E.J. Description: Crystal structure of CXCL13 [[...

New page

'''Unreleased structure'''

The entry 7jny is ON HOLD

Authors: Rosenberg Jr., E.M., Rajasekaran, D., Murphy, J.W., Pantouris, G., Lolis, E.J.

Description: Crystal structure of CXCL13
[[Category: Unreleased Structures]]
[[Category: Rosenberg Jr]]
[[Category: Rajasekaran, D]]
[[Category: Lolis, E.J]]
[[Category: E.M]]
[[Category: Murphy, J.W]]
[[Category: Pantouris, G]]