OCA at 15:29, 18 October 2023

OCA — Wed, 18 Oct 2023 15:29:36 GMT

←Older revision		Revision as of 15:29, 18 October 2023
Line 1:		Line 1:

-	====	+	==Crystal structure of Ruminococcus gnavus immunoglobulin binding protein in complex with 338E6 Fab==
-	<StructureSection load='7kpj' size='340' side='right'caption='[[7kpj]]' scene=''>	+	<StructureSection load='7kpj' size='340' side='right'caption='[[7kpj]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<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>	+	<table><tr><td colspan='2'>[[7kpj]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Ruminococcus_gnavus Ruminococcus gnavus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KPJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KPJ FirstGlance]. <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=7kpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kpj OCA], [https://pdbe.org/7kpj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kpj RCSB], [https://www.ebi.ac.uk/pdbsum/7kpj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kpj ProSAT]</span></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]] 2.1Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=7kpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kpj OCA], [https://pdbe.org/7kpj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kpj RCSB], [https://www.ebi.ac.uk/pdbsum/7kpj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kpj ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A2N5NGA8_RUMGN A0A2N5NGA8_RUMGN]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Microorganisms have coevolved diverse mechanisms to impair host defenses. A major one, superantigens, can result in devastating effects on the immune system. While all known superantigens induce vast immune cell proliferation and come from opportunistic pathogens, recently, proteins with similar broad specificity to antibody variable (V) domain families were identified in a commensal microbiota. These proteins, identified in the human commensal Ruminococcus gnavus, are called immunoglobulin-binding protein (Ibp) A and B and have been shown to activate B cells in vitro expressing either human VH3 or murine VH5/6/7. Here, we provide molecular and functional studies revealing the basis of this Ibp/immunoglobulin (Ig) interaction. The crystal structure and biochemical assays of a truncated IbpA construct in complex with mouse VH5 antigen-binding fragment (Fab) shows a binding of Ig heavy chain framework residues to the Ibp Domain D and the C-terminal heavy chain binding domain (HCBD). We used targeted mutagenesis of contact residues and affinity measurements and performed studies of the Fab-IbpA complex to determine the stoichiometry between Ibp and VH domains, suggesting Ibp may serve to cluster full-length IgA antibodies in vivo. Furthermore, in vitro stimulation experiments indicate that binding of the Ibp HCBD alone is sufficient to activate responsive murine B cell receptors. The presence of these proteins in a commensal microbe suggest that binding a broad repertoire of immunoglobulins, particularly in the gut/microbiome environment, may provide an important function in the maintenance of host/microbiome homeostasis contrasting with the pathogenic role of structurally homologous superantigens expressed by pathogens.
		+
		+	The molecular characterization of antibody binding to a superantigen-like protein from a commensal microbe.,Borowska MT, Drees C, Yarawsky AE, Viswanathan M, Ryan SM, Bunker JJ, Herr AB, Bendelac A, Adams EJ Proc Natl Acad Sci U S A. 2021 Sep 28;118(39):e2023898118. doi: , 10.1073/pnas.2023898118. PMID:34548394<ref>PMID:34548394</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7kpj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Mus musculus]]
		+	[[Category: Adams EJ]]
		+	[[Category: Borowska MT]]

OCA at 07:28, 19 January 2022

OCA — Wed, 19 Jan 2022 07:28:13 GMT

←Older revision		Revision as of 07:28, 19 January 2022
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7kpj ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7kpj' size='340' side='right'caption='[[7kpj]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<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>
-	~~Description~~:	+	</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=7kpj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kpj OCA], [https://pdbe.org/7kpj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kpj RCSB], [https://www.ebi.ac.uk/pdbsum/7kpj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kpj ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 11:11, 16 December 2020

OCA — Wed, 16 Dec 2020 11:11:49 GMT

←Older revision		Revision as of 11:11, 16 December 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 18 Nov 2020 08:12:02 GMT

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

←Older revision

Revision as of 08:12, 18 November 2020

OCA: New page: '''Unreleased structure''' The entry 7kpj is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 18 Nov 2020 08:12:01 GMT

New page: '''Unreleased structure''' The entry 7kpj is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7kpj is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

7kpj - Revision history

OCA at 15:29, 18 October 2023

OCA at 07:28, 19 January 2022

OCA at 11:11, 16 December 2020

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

OCA: New page: '''Unreleased structure''' The entry 7kpj is ON HOLD Authors: Description: Category: Unreleased Structures