4l4j - Revision history

OCA at 16:11, 20 September 2023

2023-09-20T16:11:26Z

←Older revision		Revision as of 16:11, 20 September 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4l4j]] 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=4L4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4L4J FirstGlance]. <br>		<table><tr><td colspan='2'>[[4l4j]] 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=4L4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4L4J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 1.92Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=4l4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l4j OCA], [https://pdbe.org/4l4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4l4j RCSB], [https://www.ebi.ac.uk/pdbsum/4l4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4l4j ProSAT]</span></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=4l4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l4j OCA], [https://pdbe.org/4l4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4l4j RCSB], [https://www.ebi.ac.uk/pdbsum/4l4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4l4j ProSAT]</span></td></tr>
	</table>		</table>

OCA at 09:32, 7 December 2022

2022-12-07T09:32:06Z

←Older revision		Revision as of 09:32, 7 December 2022
Line 1:		Line 1:

	==Crystal structure of fc-fragment of human IgG2-Sigma antibody==		==Crystal structure of fc-fragment of human IgG2-Sigma antibody==
-	<StructureSection load='4l4j' size='340' side='right' caption='[[4l4j]], [[Resolution\|resolution]] 1.92Å' scene=''>	+	<StructureSection load='4l4j' size='340' side='right'caption='[[4l4j]], [[Resolution\|resolution]] 1.92Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4l4j]] is a 2 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=4L4J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4L4J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4l4j]] 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=4L4J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4L4J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=~~GOL~~:~~GLYCEROL~~'>~~GOL~~</scene>, <scene name='pdbligand=~~FUC~~:~~ALPHA-L-FUCOSE~~'>~~FUC~~</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4haf\|4haf]], [[4hag\|4hag]]</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=4l4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l4j OCA], [https://pdbe.org/4l4j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4l4j RCSB], [https://www.ebi.ac.uk/pdbsum/4l4j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4l4j ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IGHG2 ([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~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4l4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l4j OCA], [~~http~~://pdbe.org/4l4j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4l4j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4l4j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4l4j ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/IGHG2_HUMAN IGHG2_HUMAN]] Recurrent infections associated with rare immunoglobulin isotypes deficiency.	+	[https://www.uniprot.org/uniprot/IGHG2_HUMAN IGHG2_HUMAN] Recurrent infections associated with rare immunoglobulin isotypes deficiency.
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/IGHG2_HUMAN IGHG2_HUMAN]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
-	[[Category: ~~Gillilang, G~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Malia, T~~]]	+	[[Category: Gillilang G]]
-	[[Category: ~~Teplyakov, A~~]]	+	[[Category: Malia T]]
-	[[Category: ~~Immune system]]~~	+	[[Category: Teplyakov A]]
-	~~[[Category: Immunoglobulin fold~~]]	+

OCA at 17:35, 5 August 2016

2016-08-05T17:35:27Z

←Older revision		Revision as of 17:35, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of fc-fragment of human IgG2-Sigma antibody==		==Crystal structure of fc-fragment of human IgG2-Sigma antibody==
	<StructureSection load='4l4j' size='340' side='right' caption='[[4l4j]], [[Resolution\|resolution]] 1.92Å' scene=''>		<StructureSection load='4l4j' size='340' side='right' caption='[[4l4j]], [[Resolution\|resolution]] 1.92Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4haf\|4haf]], [[4hag\|4hag]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4haf\|4haf]], [[4hag\|4hag]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IGHG2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IGHG2 ([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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4l4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l4j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4l4j RCSB], [http://www.ebi.ac.uk/pdbsum/4l4j PDBsum]</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=4l4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l4j OCA], [http://pdbe.org/4l4j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4l4j RCSB], [http://www.ebi.ac.uk/pdbsum/4l4j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4l4j ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 18:		Line 19:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4l4j" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 20:40, 25 December 2014

2014-12-25T20:40:50Z

←Older revision		Revision as of 20:40, 25 December 2014
Line 10:		Line 10:
	== Disease ==		== Disease ==
	[[http://www.uniprot.org/uniprot/IGHG2_HUMAN IGHG2_HUMAN]] Recurrent infections associated with rare immunoglobulin isotypes deficiency.		[[http://www.uniprot.org/uniprot/IGHG2_HUMAN IGHG2_HUMAN]] Recurrent infections associated with rare immunoglobulin isotypes deficiency.
-	== Function ==
-
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 18:24, 21 December 2014

2014-12-21T18:24:26Z

←Older revision		Revision as of 18:24, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4l4j\| PDB=4l4j \| SCENE= }}~~	+	==Crystal structure of fc-fragment of human IgG2-Sigma antibody==
-	===Crystal structure of fc-fragment of human IgG2-Sigma antibody===	+	<StructureSection load='4l4j' size='340' side='right' caption='[[4l4j]], [[Resolution\|resolution]] 1.92Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23872058}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4l4j]] is a 2 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=4L4J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4L4J FirstGlance]. <br>
-	==Disease==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4haf\|4haf]], [[4hag\|4hag]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">IGHG2 ([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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4l4j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4l4j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4l4j RCSB], [http://www.ebi.ac.uk/pdbsum/4l4j PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
	[[http://www.uniprot.org/uniprot/IGHG2_HUMAN IGHG2_HUMAN]] Recurrent infections associated with rare immunoglobulin isotypes deficiency.		[[http://www.uniprot.org/uniprot/IGHG2_HUMAN IGHG2_HUMAN]] Recurrent infections associated with rare immunoglobulin isotypes deficiency.
		+	== Function ==
		+
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Fc variant of IgG2, designated as IgG2sigma, was engineered with V234A/G237A /P238S/H268A/V309L/A330S/P331S substitutions to eliminate affinity for Fcgamma receptors and C1q complement protein and consequently, immune effector functions. IgG2sigma was compared to other previously well-characterized Fc 'muted' variants, including aglycosylated IgG1, IgG2m4 (H268Q/V309L/A330S/P331S, changes to IgG4), and IgG4 ProAlaAla (S228P/L234A/L235A) in its capacity to bind FcgammaRs and activate various immune-stimulatory responses. In contrast to the previously characterized muted Fc variants, which retain selective FcgammaR binding and effector functions, IgG2sigma shows no detectable binding to the Fcgamma receptors in affinity and avidity measurements, nor any detectable antibody-dependent cytotoxicity, phagocytosis, complement activity, or Fc-mediated cytokine release. Moreover, IgG2sigma shows minimal immunogenic potential by T-cell epitope analysis. The circulating half-life of IgG2sigma in monkeys is extended relative to IgG1 and IgG2, in spite of similar in vitro binding to recombinant FcRn. The three-dimensional structure of the Fc, needed for assessing the basis for the absence of effector function, was compared with that of IgG2 revealing a number of conformational differences near the hinge region of the CH2 domain that result from the amino acid substitutions. Modeling reveals that at least one of the key interactions with FcgammaRs is disrupted by a conformational change that reorients P329 to a position that prevents it from interacting with conserved W90 and W113 residues of the FcgammaRs. Inspection of the structure also indicated significant changes to the conformations of D270 and P329 in the CH2 domain that could negatively impact C1q binding. Thus, structural perturbations of the Fc provide a rationale for the loss of function. In toto, these properties of IgG2sigma suggest that it is a superior alternative to previously described IgG variants of minimal effector function, for future therapeutic applications of non-immunostimulatory mAb and Fc-fusion platforms.

-	~~==About this Structure==~~	+	An engineered Fc variant of an IgG eliminates all immune effector functions via structural perturbations.,Vafa O, Gilliland GL, Brezski RJ, Strake B, Wilkinson T, Lacy ER, Scallon B, Teplyakov A, Malia TJ, Strohl WR Methods. 2013 Jul 17. pii: S1046-2023(13)00247-8. doi:, 10.1016/j.ymeth.2013.06.035. PMID:23872058<ref>PMID:23872058</ref>
-	~~[[4l4j]] is a 2 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=4L4J OCA]~~.	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023872058</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Human]]		[[Category: Human]]
-	[[Category: Gillilang, G.]]	+	[[Category: Gillilang, G]]
-	[[Category: Malia, T.]]	+	[[Category: Malia, T]]
-	[[Category: Teplyakov, A.]]	+	[[Category: Teplyakov, A]]
	[[Category: Immune system]]		[[Category: Immune system]]
	[[Category: Immunoglobulin fold]]		[[Category: Immunoglobulin fold]]

OCA at 05:43, 22 January 2014

2014-01-22T05:43:14Z

←Older revision		Revision as of 05:43, 22 January 2014
Line 7:		Line 7:

	==About this Structure==		==About this Structure==
-	[[4l4j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L4J OCA].	+	[[4l4j]] is a 2 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=4L4J OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:023872058</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:023872058</ref><references group="xtra"/><references/>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Gillilang, G.]]		[[Category: Gillilang, G.]]
	[[Category: Malia, T.]]		[[Category: Malia, T.]]

OCA at 07:26, 28 August 2013

2013-08-28T07:26:50Z

←Older revision		Revision as of 07:26, 28 August 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4l4j\| PDB=4l4j \| SCENE= }}
		+	===Crystal structure of fc-fragment of human IgG2-Sigma antibody===
		+	{{ABSTRACT_PUBMED_23872058}}

-	~~The entry 4l4j is ON HOLD~~ ~~until Paper Publication~~	+	==Disease==
		+	[[http://www.uniprot.org/uniprot/IGHG2_HUMAN IGHG2_HUMAN]] Recurrent infections associated with rare immunoglobulin isotypes deficiency.

-	~~Authors~~: ~~Teplyakov, A~~.~~, Malia, T~~.~~, Gillilang, G~~.	+	==About this Structure==
		+	[[4l4j]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4L4J OCA].

-	~~Description~~: ~~Crystal structure of fc-fragment of human IgG2-Sigma antibody~~	+	==Reference==
		+	<ref group="xtra">PMID:023872058</ref><references group="xtra"/><references/>
		+	[[Category: Homo sapiens]]
		+	[[Category: Gillilang, G.]]
		+	[[Category: Malia, T.]]
		+	[[Category: Teplyakov, A.]]
		+	[[Category: Immune system]]
		+	[[Category: Immunoglobulin fold]]

OCA at 04:13, 1 August 2013

2013-08-01T04:13:58Z

←Older revision		Revision as of 04:13, 1 August 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4l4j is ON HOLD	+	The entry 4l4j is ON HOLD until Paper Publication

	Authors: Teplyakov, A., Malia, T., Gillilang, G.		Authors: Teplyakov, A., Malia, T., Gillilang, G.

	Description: Crystal structure of fc-fragment of human IgG2-Sigma antibody		Description: Crystal structure of fc-fragment of human IgG2-Sigma antibody

OCA at 15:05, 10 July 2013

2013-07-10T15:05:53Z

←Older revision		Revision as of 15:05, 10 July 2013
Line 5:		Line 5:
	Authors: Teplyakov, A., Malia, T., Gillilang, G.		Authors: Teplyakov, A., Malia, T., Gillilang, G.

-	Description: ~~CRYSTAL STRUCTURE OF FC~~-~~FRAGMENT OF HUMAN IGG2~~-~~SIGMA ANTIBODY~~	+	Description: Crystal structure of fc-fragment of human IgG2-Sigma antibody

OCA: Protected "4l4j" [edit=sysop:move=sysop]

2013-06-19T12:30:19Z

Protected "4l4j" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:30, 19 June 2013