4u0b - Revision history

OCA at 12:25, 20 December 2023

OCA — Wed, 20 Dec 2023 12:25:50 GMT

←Older revision		Revision as of 12:25, 20 December 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4u0b]] is a 24 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_type_1_(NEW_YORK-5_ISOLATE) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U0B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4U0B FirstGlance]. <br>		<table><tr><td colspan='2'>[[4u0b]] is a 24 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_type_1_(NEW_YORK-5_ISOLATE) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U0B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4U0B 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=4u0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u0b OCA], [https://pdbe.org/4u0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4u0b RCSB], [https://www.ebi.ac.uk/pdbsum/4u0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4u0b 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]] 2.8Å</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=4u0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u0b OCA], [https://pdbe.org/4u0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4u0b RCSB], [https://www.ebi.ac.uk/pdbsum/4u0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4u0b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:54, 22 March 2023

OCA — Wed, 22 Mar 2023 07:54:18 GMT

←Older revision		Revision as of 07:54, 22 March 2023
Line 3:		Line 3:
	<StructureSection load='4u0b' size='340' side='right'caption='[[4u0b]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='4u0b' size='340' side='right'caption='[[4u0b]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4u0b]] is a 24 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Hiv~~-1 ~~Hiv~~-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U0B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4U0B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4u0b]] is a 24 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_type_1_(NEW_YORK-5_ISOLATE) Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U0B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4U0B FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4u0a\|4u0a]]</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=4u0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u0b OCA], [https://pdbe.org/4u0b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4u0b RCSB], [https://www.ebi.ac.uk/pdbsum/4u0b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4u0b ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gag ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11698 HIV-1])</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=4u0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u0b OCA], [~~http~~://pdbe.org/4u0b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4u0b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4u0b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4u0b ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/GAG_HV1N5 GAG_HV1N5]] Matrix protein p17 targets Gag and Gag-Pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex. Implicated in the release from host cell mediated by Vpu. Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex. Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers. p6-gag plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1 (By similarity). [[http://www.uniprot.org/uniprot/CPSF6_HUMAN CPSF6_HUMAN]] Component of the cleavage factor Im complex (CFIm) that plays a key role in pre-mRNA 3'-processing. Involved in association with NUDT21/CPSF5 in pre-MRNA 3'-end poly(A) site cleavage and poly(A) addition. CPSF6 binds to cleavage and polyadenylation RNA substrates and promotes RNA looping.<ref>PMID:9659921</ref> <ref>PMID:8626397</ref> <ref>PMID:14690600</ref> <ref>PMID:20695905</ref> <ref>PMID:21295486</ref>	+	[https://www.uniprot.org/uniprot/GAG_HV1N5 GAG_HV1N5] Matrix protein p17 targets Gag and Gag-Pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex. Implicated in the release from host cell mediated by Vpu. Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex. Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers. p6-gag plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1 (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 4u0b" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4u0b" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Hiv-1~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jacques~~, D A~~]]	+	[[Category: Jacques DA]]
-	[[Category: James~~, L C~~]]	+	[[Category: James LC]]
-	[[Category: Price~~, A J]]~~	+	[[Category: Price AJ]]
-	~~[[Category: Capsid]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 14:08, 10 May 2019

OCA — Fri, 10 May 2019 14:08:07 GMT

←Older revision		Revision as of 14:08, 10 May 2019
Line 1:		Line 1:

	==Hexamer HIV-1 CA in complex with CPSF6 peptide, P212121 crystal form==		==Hexamer HIV-1 CA in complex with CPSF6 peptide, P212121 crystal form==
-	<StructureSection load='4u0b' size='340' side='right' caption='[[4u0b]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='4u0b' size='340' side='right'caption='[[4u0b]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4u0b]] is a 24 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U0B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U0B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4u0b]] is a 24 chain structure with sequence from [http://en.wikipedia.org/wiki/Hiv-1 Hiv-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U0B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U0B FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4u0a\|4u0a]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4u0a\|4u0a]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gag ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11698 HIV-1])</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=4u0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u0b OCA], [http://pdbe.org/4u0b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4u0b RCSB], [http://www.ebi.ac.uk/pdbsum/4u0b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4u0b 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=4u0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u0b OCA], [http://pdbe.org/4u0b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4u0b RCSB], [http://www.ebi.ac.uk/pdbsum/4u0b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4u0b ProSAT]</span></td></tr>
	</table>		</table>
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Hiv-1]]
		+	[[Category: Large Structures]]
	[[Category: Jacques, D A]]		[[Category: Jacques, D A]]
	[[Category: James, L C]]		[[Category: James, L C]]

OCA at 09:53, 4 August 2016

OCA — Thu, 04 Aug 2016 09:53:07 GMT

←Older revision		Revision as of 09:53, 4 August 2016
Line 1:		Line 1:
		+
	==Hexamer HIV-1 CA in complex with CPSF6 peptide, P212121 crystal form==		==Hexamer HIV-1 CA in complex with CPSF6 peptide, P212121 crystal form==
	<StructureSection load='4u0b' size='340' side='right' caption='[[4u0b]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='4u0b' size='340' side='right' caption='[[4u0b]], [[Resolution\|resolution]] 2.80Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4u0b]] is a 24 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U0B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U0B FirstGlance]. <br>		<table><tr><td colspan='2'>[[4u0b]] is a 24 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U0B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U0B FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4u0a\|4u0a]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4u0a\|4u0a]]</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=4u0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u0b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4u0b RCSB], [http://www.ebi.ac.uk/pdbsum/4u0b 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=4u0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u0b OCA], [http://pdbe.org/4u0b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4u0b RCSB], [http://www.ebi.ac.uk/pdbsum/4u0b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4u0b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	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 4u0b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:35, 24 December 2014

OCA — Wed, 24 Dec 2014 08:35:00 GMT

←Older revision		Revision as of 08:35, 24 December 2014
Line 6:		Line 6:
	<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=4u0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u0b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4u0b RCSB], [http://www.ebi.ac.uk/pdbsum/4u0b 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=4u0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u0b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4u0b RCSB], [http://www.ebi.ac.uk/pdbsum/4u0b PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GAG_HV1N5 GAG_HV1N5]] Matrix protein p17 targets Gag and Gag-Pol polyproteins to the plasma membrane via a multipartite membrane binding signal, that includes its myristoylated N-terminus. Also mediates nuclear localization of the preintegration complex. Implicated in the release from host cell mediated by Vpu. Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex. Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers. p6-gag plays a role in budding of the assembled particle by interacting with the host class E VPS proteins TSG101 and PDCD6IP/AIP1 (By similarity). [[http://www.uniprot.org/uniprot/CPSF6_HUMAN CPSF6_HUMAN]] Component of the cleavage factor Im complex (CFIm) that plays a key role in pre-mRNA 3'-processing. Involved in association with NUDT21/CPSF5 in pre-MRNA 3'-end poly(A) site cleavage and poly(A) addition. CPSF6 binds to cleavage and polyadenylation RNA substrates and promotes RNA looping.<ref>PMID:9659921</ref> <ref>PMID:8626397</ref> <ref>PMID:14690600</ref> <ref>PMID:20695905</ref> <ref>PMID:21295486</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 07:01, 12 November 2014

OCA — Wed, 12 Nov 2014 07:01:11 GMT

←Older revision		Revision as of 07:01, 12 November 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Hexamer HIV-1 CA in complex with CPSF6 peptide, P212121 crystal form==
		+	<StructureSection load='4u0b' size='340' side='right' caption='[[4u0b]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4u0b]] is a 24 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4U0B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4U0B FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4u0a\|4u0a]]</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=4u0b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4u0b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4u0b RCSB], [http://www.ebi.ac.uk/pdbsum/4u0b PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The HIV-1 capsid is involved in all infectious steps from reverse transcription to integration site selection, and is the target of multiple host cell and pharmacologic ligands. However, structural studies have been limited to capsid monomers (CA), and the mechanistic basis for how these ligands influence infection is not well understood. Here we show that a multi-subunit interface formed exclusively within CA hexamers mediates binding to linear epitopes within cellular cofactors NUP153 and CPSF6, and is competed for by the antiretroviral compounds PF74 and BI-2. Each ligand is anchored via a shared phenylalanine-glycine (FG) motif to a pocket within the N-terminal domain of one monomer, and all but BI-2 also make essential interactions across the N-terminal domain: C-terminal domain (NTD:CTD) interface to a second monomer. Dissociation of hexamer into CA monomers prevents high affinity interaction with CPSF6 and PF74, and abolishes binding to NUP153. The second interface is conformationally dynamic, but binding of NUP153 or CPSF6 peptides is accommodated by only one conformation. NUP153 and CPSF6 have overlapping binding sites, but each makes unique CA interactions that, when mutated selectively, perturb cofactor dependency. These results reveal that multiple ligands share an overlapping interface in HIV-1 capsid that is lost upon viral disassembly.

-	~~The entry 4u0b is ON HOLD until Paper Publication~~	+	Host Cofactors and Pharmacologic Ligands Share an Essential Interface in HIV-1 Capsid That Is Lost upon Disassembly.,Price AJ, Jacques DA, McEwan WA, Fletcher AJ, Essig S, Chin JW, Halambage UD, Aiken C, James LC PLoS Pathog. 2014 Oct 30;10(10):e1004459. doi: 10.1371/journal.ppat.1004459., eCollection 2014 Oct. PMID:25356722<ref>PMID:25356722</ref>

-	~~Authors: Price~~, A.J., Jacques, D.A., James, L.C.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~:	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Jacques, D A]]
		+	[[Category: James, L C]]
		+	[[Category: Price, A J]]
		+	[[Category: Capsid]]
		+	[[Category: Complex]]
		+	[[Category: Viral protein]]

OCA: Protected "4u0b" [edit=sysop:move=sysop]

OCA — Wed, 23 Jul 2014 07:23:50 GMT

Protected "4u0b" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:23, 23 July 2014

OCA: New page: '''Unreleased structure''' The entry 4u0b is ON HOLD until Paper Publication Authors: Price, A.J., Jacques, D.A., James, L.C. Description:

OCA — Wed, 23 Jul 2014 07:23:49 GMT

New page: '''Unreleased structure''' The entry 4u0b is ON HOLD until Paper Publication Authors: Price, A.J., Jacques, D.A., James, L.C. Description:

New page

'''Unreleased structure'''

The entry 4u0b is ON HOLD until Paper Publication

Authors: Price, A.J., Jacques, D.A., James, L.C.

Description: