5d1x - Revision history

OCA at 10:18, 21 June 2023

OCA — Wed, 21 Jun 2023 10:18:29 GMT

←Older revision		Revision as of 10:18, 21 June 2023
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	<StructureSection load='5d1x' size='340' side='right'caption='[[5d1x]], [[Resolution\|resolution]] 3.21Å' scene=''>		<StructureSection load='5d1x' size='340' side='right'caption='[[5d1x]], [[Resolution\|resolution]] 3.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d1x]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~] and [~~http~~://en.wikipedia.org/wiki/~~Staa3 Staa3~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D1X OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5D1X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d1x]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Staphylococcus_aureus_subsp._aureus_USA300 Staphylococcus aureus subsp. aureus USA300]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D1X OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5D1X FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d1q\|5d1q]], [[5d1z\|5d1z]]</td></tr>~~	+	</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=5d1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d1x OCA], [https://pdbe.org/5d1x PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5d1x RCSB], [https://www.ebi.ac.uk/pdbsum/5d1x PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5d1x ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">isdB, frpB, sasJ, sirH, SAUSA300_1028 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=367830 STAA3])</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=5d1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d1x OCA], [~~http~~://pdbe.org/5d1x PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5d1x RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5d1x PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5d1x ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~ISDB_STAA3 ISDB_STAA3~~]~~] Seems to function as the primary~~ receptor ~~for hemoglobin since its inactivation inhibits the ability of S.aureus~~ to ~~bind hemoglobin. Binds hemoglobin in a dose-dependent way. Required for S.aureus~~ growth ~~using~~ hemoglobin as ~~the~~ sole iron source. ~~Also required~~ for ~~virulence~~. ~~IsdA and/or IsdB promote~~ resistance to hydrogen peroxide and killing by neutrophils ~~(By similarity)~~.	+	[https://www.uniprot.org/uniprot/ISDB_STAA8 ISDB_STAA8] Cell wall-anchored surface receptor that extracts heme from oxidized metHb to enable growth on hemoglobin as a sole iron source. Rapidly extracts heme from hemoglobin and transfers it to IsdA or IsdC, which then relays it to the membrane transporter/IsdEF for internalization. Promotes also resistance to hydrogen peroxide and killing by neutrophils.[UniProtKB:A6QG30]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Staa3~~]]	+	[[Category: Staphylococcus aureus subsp. aureus USA300]]
-	[[Category: Deng, X]]	+	[[Category: Deng X]]
-	~~[[Category: Germline encoded]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Isdb]]~~	+
-	~~[[Category: Neat2~~]]	+

OCA at 10:33, 1 April 2020

OCA — Wed, 01 Apr 2020 10:33:38 GMT

←Older revision		Revision as of 10:33, 1 April 2020
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	==IsdB NEAT2 bound by D4-30==		==IsdB NEAT2 bound by D4-30==
-	<StructureSection load='5d1x' size='340' side='right' caption='[[5d1x]], [[Resolution\|resolution]] 3.21Å' scene=''>	+	<StructureSection load='5d1x' size='340' side='right'caption='[[5d1x]], [[Resolution\|resolution]] 3.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5d1x]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D1X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D1X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5d1x]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Staa3 Staa3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D1X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D1X FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d1q\|5d1q]], [[5d1z\|5d1z]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d1q\|5d1q]], [[5d1z\|5d1z]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">isdB, frpB, sasJ, sirH, SAUSA300_1028 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=367830 STAA3])</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=5d1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d1x OCA], [http://pdbe.org/5d1x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d1x RCSB], [http://www.ebi.ac.uk/pdbsum/5d1x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d1x 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=5d1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d1x OCA], [http://pdbe.org/5d1x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d1x RCSB], [http://www.ebi.ac.uk/pdbsum/5d1x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d1x ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
		+	[[Category: Staa3]]
	[[Category: Deng, X]]		[[Category: Deng, X]]
	[[Category: Germline encoded]]		[[Category: Germline encoded]]

OCA at 19:37, 9 December 2016

OCA — Fri, 09 Dec 2016 19:37:08 GMT

←Older revision		Revision as of 19:37, 9 December 2016
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	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/ISDB_STAA3 ISDB_STAA3]] Seems to function as the primary receptor for hemoglobin since its inactivation inhibits the ability of S.aureus to bind hemoglobin. Binds hemoglobin in a dose-dependent way. Required for S.aureus growth using hemoglobin as the sole iron source. Also required for virulence. IsdA and/or IsdB promote resistance to hydrogen peroxide and killing by neutrophils (By similarity).		[[http://www.uniprot.org/uniprot/ISDB_STAA3 ISDB_STAA3]] Seems to function as the primary receptor for hemoglobin since its inactivation inhibits the ability of S.aureus to bind hemoglobin. Binds hemoglobin in a dose-dependent way. Required for S.aureus growth using hemoglobin as the sole iron source. Also required for virulence. IsdA and/or IsdB promote resistance to hydrogen peroxide and killing by neutrophils (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Staphylococcus aureus is both an important pathogen and a human commensal. To explore this ambivalent relationship between host and microbe, we analysed the memory humoral response against IsdB, a protein involved in iron acquisition, in four healthy donors. Here we show that in all donors a heavily biased use of two immunoglobulin heavy chain germlines generated high affinity (pM) antibodies that neutralize the two IsdB NEAT domains, IGHV4-39 for NEAT1 and IGHV1-69 for NEAT2. In contrast to the typical antibody/antigen interactions, the binding is primarily driven by the germline-encoded hydrophobic CDRH-2 motifs of IGHV1-69 and IGHV4-39, with a binding mechanism nearly identical for each antibody derived from different donors. Our results suggest that IGHV1-69 and IGHV4-39, while part of the adaptive immune system, may have evolved under selection pressure to encode a binding motif innately capable of recognizing and neutralizing a structurally conserved protein domain involved in pathogen iron acquisition.
		+
		+	Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire.,Yeung YA, Foletti D, Deng X, Abdiche Y, Strop P, Glanville J, Pitts S, Lindquist K, Sundar PD, Sirota M, Hasa-Moreno A, Pham A, Melton Witt J, Ni I, Pons J, Shelton D, Rajpal A, Chaparro-Riggers J Nat Commun. 2016 Nov 18;7:13376. doi: 10.1038/ncomms13376. PMID:27857134<ref>PMID:27857134</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5d1x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 16:21, 10 August 2016

OCA — Wed, 10 Aug 2016 16:21:32 GMT

←Older revision		Revision as of 16:21, 10 August 2016
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-	'''Unreleased structure'''

-	~~The entry~~ 5d1x ~~is ON HOLD until Paper Publication~~	+	==IsdB NEAT2 bound by D4-30==
-		+	<StructureSection load='5d1x' size='340' side='right' caption='[[5d1x]], [[Resolution\|resolution]] 3.21Å' scene=''>
-	~~Authors~~: ~~Deng, X~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5d1x]] is a 5 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5D1X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5D1X FirstGlance]. <br>
-	~~Description~~: ~~IsdB NEAT2 bound by D4~~-30	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5d1q\|5d1q]], [[5d1z\|5d1z]]</td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=5d1x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5d1x OCA], [http://pdbe.org/5d1x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5d1x RCSB], [http://www.ebi.ac.uk/pdbsum/5d1x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5d1x ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ISDB_STAA3 ISDB_STAA3]] Seems to function as the primary receptor for hemoglobin since its inactivation inhibits the ability of S.aureus to bind hemoglobin. Binds hemoglobin in a dose-dependent way. Required for S.aureus growth using hemoglobin as the sole iron source. Also required for virulence. IsdA and/or IsdB promote resistance to hydrogen peroxide and killing by neutrophils (By similarity).
		+	__TOC__
		+	</StructureSection>
	[[Category: Deng, X]]		[[Category: Deng, X]]
		+	[[Category: Germline encoded]]
		+	[[Category: Immune system]]
		+	[[Category: Isdb]]
		+	[[Category: Neat2]]

OCA at 05:00, 14 July 2016

OCA — Thu, 14 Jul 2016 05:00:10 GMT

←Older revision		Revision as of 05:00, 14 July 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5d1x is ON HOLD	+	The entry 5d1x is ON HOLD until Paper Publication

	Authors: Deng, X.		Authors: Deng, X.

OCA at 09:48, 2 March 2016

OCA — Wed, 02 Mar 2016 09:48:25 GMT

←Older revision		Revision as of 09:48, 2 March 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5d1x is ON HOLD ~~until Paper Publication~~	+	The entry 5d1x is ON HOLD

	Authors: Deng, X.		Authors: Deng, X.

OCA at 12:25, 10 February 2016

OCA — Wed, 10 Feb 2016 12:25:40 GMT

←Older revision		Revision as of 12:25, 10 February 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5d1x is ON HOLD	+	The entry 5d1x is ON HOLD until Paper Publication

	Authors: Deng, X.		Authors: Deng, X.

OCA at 10:45, 9 December 2015

OCA — Wed, 09 Dec 2015 10:45:10 GMT

←Older revision		Revision as of 10:45, 9 December 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5d1x is ON HOLD ~~until Paper Publication~~	+	The entry 5d1x is ON HOLD

	Authors: Deng, X.		Authors: Deng, X.

OCA at 11:16, 20 August 2015

OCA — Thu, 20 Aug 2015 11:16:50 GMT

←Older revision		Revision as of 11:16, 20 August 2015
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5d1x is ON HOLD	+	The entry 5d1x is ON HOLD until Paper Publication

	Authors: Deng, X.		Authors: Deng, X.

-	Description: IsdB NEAT2 bound by ~~clone~~ D4-30	+	Description: IsdB NEAT2 bound by D4-30
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Deng, X]]		[[Category: Deng, X]]

OCA: Protected "5d1x" [edit=sysop:move=sysop]

OCA — Wed, 12 Aug 2015 13:43:19 GMT

Protected "5d1x" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:43, 12 August 2015