2ec7 - Revision history

OCA at 06:39, 1 May 2024

2024-05-01T06:39:45Z

← Older revision		Revision as of 06:39, 1 May 2024
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	==Solution Structure of Human Immunodificiency Virus Type-2 Nucleocapsid Protein==		==Solution Structure of Human Immunodificiency Virus Type-2 Nucleocapsid Protein==
	<StructureSection load='2ec7' size='340' side='right'caption='[[2ec7~~]], [[NMR_Ensembles_of_Models \| 11 NMR models~~]]' scene=''>		<StructureSection load='2ec7' size='340' side='right'caption='[[2ec7]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ec7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Hiv~~-2 ~~Hiv~~-2]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EC7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ec7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_type_2_(ISOLATE_GHANA-1) Human immunodeficiency virus type 2 (ISOLATE GHANA-1)]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EC7 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[1nc8\|1nc8]], [[2e1x\|2e1x]], [[2di2\|2di2]]~~</~~div~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2ec7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ec7 OCA], [https://pdbe.org/2ec7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ec7 RCSB], [https://www.ebi.ac.uk/pdbsum/2ec7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ec7 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=2ec7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ec7 OCA], [https://pdbe.org/2ec7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ec7 RCSB], [https://www.ebi.ac.uk/pdbsum/2ec7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ec7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/GAG_HV2G1 GAG_HV2G1]] Matrix protein p17 targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal. Also mediates nuclear localization of the preintegration complex (By similarity). Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex (By similarity). Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers (By similarity). 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).		[https://www.uniprot.org/uniprot/GAG_HV2G1 GAG_HV2G1] Matrix protein p17 targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal. Also mediates nuclear localization of the preintegration complex (By similarity). Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex (By similarity). Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers (By similarity). 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).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ec7 ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ec7 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The nucleocapsid (NC) protein of HIV, which contains two CCHC-type zinc fingers connected by a linker, is a multifunctional protein involved in many of the critical steps of the HIV life cycle. HIV-1 and HIV-2 contain NC proteins NCp7 and NCp8, respectively. The amino acid sequences of both NC proteins are 67% identical. For NCp7, the important elements for RNA binding were found to be the first zinc finger flanked by the linker, as the minimal active domain, and the 3(10) helix in the N-terminus, as the secondary active domain. However, for the NCp8 counterpart in HIV-2, the mechanism for binding to viral RNA has not yet been clarified. In this study, we determined NCp8's three-dimensional structure for the first time and examined the dynamic behavior and chemical shift perturbation as a function of the concentration of viral RNA SL3. Moreover, the specific binding activities of NCp8 and the NCp8-derived peptides with SL3 were examined by a native polyacrylamide gel electrophoresis assay. These results indicate that the RNA recognition mechanism for NCp8 is different from that of NCp7 and that the hydrophobic cleft in the second zinc finger acts as a secondary active domain instead of the 3(10) helix in NCp7. Furthermore, the flexibility of the linker is limited by the hydrogen bond between the first zinc finger (Asn11) and the linker (Arg27), which makes it possible for the sites around Trp10 in the minimal active domain and the secondary active domain to form the binding surface.

	The RNA recognition mechanism of human immunodeficiency virus (HIV) type 2 NCp8 is different from that of HIV-1 NCp7.,Matsui T, Tanaka T, Endoh H, Sato K, Tanaka H, Miyauchi E, Kawashima Y, Nagai-Makabe M, Komatsu H, Kohno T, Maeda T, Kodera Y Biochemistry. 2009 May 26;48(20):4314-23. PMID:19334676<ref>PMID:19334676</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2ec7" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[Gag polyprotein 3D structures\|Gag polyprotein 3D structures]]		*[[Gag polyprotein 3D structures\|Gag polyprotein 3D structures]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Hiv-2]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Endoh, H]]		[[Category: Endoh H]]
	[[Category: Kodera, Y]]		[[Category: Kodera Y]]
	[[Category: Kohno, T]]		[[Category: Kohno T]]
	[[Category: Komatsu, H]]		[[Category: Komatsu H]]
	[[Category: Maeda, T]]		[[Category: Maeda T]]
	[[Category: Matsui, T]]		[[Category: Matsui T]]
	[[Category: Miyauchi, E]]		[[Category: Miyauchi E]]
	[[Category: Tanaka, H]]		[[Category: Tanaka H]]
	[[Category: Tanaka, T]]		[[Category: Tanaka T]]
	~~[[Category: Nucleocapsid protein]]~~
	~~[[Category: Rna recognition]]~~
	~~[[Category: Viral protein]]~~
	~~[[Category: Zinc finger~~]]

OCA at 20:38, 20 October 2021

2021-10-20T20:38:49Z

← Older revision		Revision as of 20:38, 20 October 2021
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	<StructureSection load='2ec7' size='340' side='right'caption='[[2ec7]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>		<StructureSection load='2ec7' size='340' side='right'caption='[[2ec7]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ec7]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Hiv-2 Hiv-2]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EC7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2EC7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ec7]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Hiv-2 Hiv-2]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EC7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EC7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nc8\|1nc8]], [[2e1x\|2e1x]], [[2di2\|2di2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1nc8\|1nc8]], [[2e1x\|2e1x]], [[2di2\|2di2]]</div></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=2ec7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ec7 OCA], [~~http~~://pdbe.org/2ec7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2ec7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2ec7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2ec7 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=2ec7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ec7 OCA], [https://pdbe.org/2ec7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ec7 RCSB], [https://www.ebi.ac.uk/pdbsum/2ec7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ec7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/GAG_HV2G1 GAG_HV2G1]] Matrix protein p17 targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal. Also mediates nuclear localization of the preintegration complex (By similarity). Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex (By similarity). Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers (By similarity). 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).		[[https://www.uniprot.org/uniprot/GAG_HV2G1 GAG_HV2G1]] Matrix protein p17 targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal. Also mediates nuclear localization of the preintegration complex (By similarity). Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex (By similarity). Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers (By similarity). 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).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 15:30, 11 December 2019

2019-12-11T15:30:29Z

← Older revision		Revision as of 15:30, 11 December 2019
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	==Solution Structure of Human Immunodificiency Virus Type-2 Nucleocapsid Protein==		==Solution Structure of Human Immunodificiency Virus Type-2 Nucleocapsid Protein==
	<StructureSection load='2ec7' size='340' side='right' caption='[[2ec7]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>		<StructureSection load='2ec7' size='340' side='right'caption='[[2ec7]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ec7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hiv-2 Hiv-2]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EC7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EC7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ec7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hiv-2 Hiv-2]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EC7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EC7 FirstGlance]. <br>
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	==See Also==		==See Also==
	*[[Gag polyprotein\|Gag polyprotein]]		*[[Gag polyprotein 3D structures\|Gag polyprotein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Hiv-2]]		[[Category: Hiv-2]]
			[[Category: Large Structures]]
	[[Category: Endoh, H]]		[[Category: Endoh, H]]
	[[Category: Kodera, Y]]		[[Category: Kodera, Y]]

OCA at 06:57, 6 June 2018

2018-06-06T06:57:23Z

← Older revision		Revision as of 06:57, 6 June 2018
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	==Solution Structure of Human Immunodificiency Virus Type-2 Nucleocapsid Protein==		==Solution Structure of Human Immunodificiency Virus Type-2 Nucleocapsid Protein==
	<StructureSection load='2ec7' size='340' side='right' caption='[[2ec7]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>		<StructureSection load='2ec7' size='340' side='right' caption='[[2ec7]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nc8\|1nc8]], [[2e1x\|2e1x]], [[2di2\|2di2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nc8\|1nc8]], [[2e1x\|2e1x]], [[2di2\|2di2]]</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=2ec7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ec7 OCA], [http://pdbe.org/2ec7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ec7 RCSB], [http://www.ebi.ac.uk/pdbsum/2ec7 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=2ec7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ec7 OCA], [http://pdbe.org/2ec7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ec7 RCSB], [http://www.ebi.ac.uk/pdbsum/2ec7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2ec7 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ec/2ec7_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ec/2ec7_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 09:45, 8 February 2016

2016-02-08T09:45:33Z

← Older revision		Revision as of 09:45, 8 February 2016
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2ec7 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 10:21, 10 September 2015

2015-09-10T10:21:12Z

← Older revision		Revision as of 10:21, 10 September 2015
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	<StructureSection load='2ec7' size='340' side='right' caption='[[2ec7]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>		<StructureSection load='2ec7' size='340' side='right' caption='[[2ec7]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ec7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Human_immunodeficiency_virus_type_2_(isolate_ghana~~-~~1) Human immunodeficiency virus type~~ 2 ~~(isolate ghana~~-1)]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EC7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EC7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ec7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Hiv-2 Hiv-2]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EC7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EC7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nc8\|1nc8]], [[2e1x\|2e1x]], [[2di2\|2di2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nc8\|1nc8]], [[2e1x\|2e1x]], [[2di2\|2di2]]</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=2ec7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ec7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ec7 RCSB], [http://www.ebi.ac.uk/pdbsum/2ec7 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=2ec7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ec7 OCA], [http://pdbe.org/2ec7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ec7 RCSB], [http://www.ebi.ac.uk/pdbsum/2ec7 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	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 2ec7" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Hiv-2]]
	[[Category: Endoh, H]]		[[Category: Endoh, H]]
	[[Category: Kodera, Y]]		[[Category: Kodera, Y]]
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	[[Category: Tanaka, H]]		[[Category: Tanaka, H]]
	[[Category: Tanaka, T]]		[[Category: Tanaka, T]]
	~~[[Category: Hiv-2]]~~
	[[Category: Nucleocapsid protein]]		[[Category: Nucleocapsid protein]]
	[[Category: Rna recognition]]		[[Category: Rna recognition]]
	[[Category: Viral protein]]		[[Category: Viral protein]]
	[[Category: Zinc finger]]		[[Category: Zinc finger]]

OCA at 22:24, 24 December 2014

2014-12-24T22:24:45Z

← Older revision		Revision as of 22:24, 24 December 2014
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2ec7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_type_2_(isolate_ghana-1) Human immunodeficiency virus type 2 (isolate ghana-1)]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EC7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EC7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2ec7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_type_2_(isolate_ghana-1) Human immunodeficiency virus type 2 (isolate ghana-1)]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EC7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EC7 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nc8\|1nc8]], [[2e1x\|2e1x]], [[2di2\|2di2]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nc8\|1nc8]], [[2e1x\|2e1x]], [[2di2\|2di2]]</td></tr>
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ec7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ec7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ec7 RCSB], [http://www.ebi.ac.uk/pdbsum/2ec7 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=2ec7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ec7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ec7 RCSB], [http://www.ebi.ac.uk/pdbsum/2ec7 PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/GAG_HV2G1 GAG_HV2G1]] Matrix protein p17 targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane binding signal. Also mediates nuclear localization of the preintegration complex (By similarity). Capsid protein p24 forms the conical core of the virus that encapsulates the genomic RNA-nucleocapsid complex (By similarity). Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers (By similarity). 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).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Endoh, H.]]		[[Category: Endoh, H]]
	[[Category: Kodera, Y.]]		[[Category: Kodera, Y]]
	[[Category: Kohno, T.]]		[[Category: Kohno, T]]
	[[Category: Komatsu, H.]]		[[Category: Komatsu, H]]
	[[Category: Maeda, T.]]		[[Category: Maeda, T]]
	[[Category: Matsui, T.]]		[[Category: Matsui, T]]
	[[Category: Miyauchi, E.]]		[[Category: Miyauchi, E]]
	[[Category: Tanaka, H.]]		[[Category: Tanaka, H]]
	[[Category: Tanaka, T.]]		[[Category: Tanaka, T]]
	[[Category: Hiv-2]]		[[Category: Hiv-2]]
	[[Category: Nucleocapsid protein]]		[[Category: Nucleocapsid protein]]

OCA at 02:28, 29 September 2014

2014-09-29T02:28:11Z

← Older revision		Revision as of 02:28, 29 September 2014
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	[[Image:~~2ec7~~.~~png~~\|~~left~~\|~~200px~~]]		==Solution Structure of Human Immunodificiency Virus Type-2 Nucleocapsid Protein==
			<StructureSection load='2ec7' size='340' side='right' caption='[[2ec7]], [[NMR_Ensembles_of_Models \| 11 NMR models]]' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2ec7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_type_2_(isolate_ghana-1) Human immunodeficiency virus type 2 (isolate ghana-1)]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EC7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2EC7 FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1nc8\|1nc8]], [[2e1x\|2e1x]], [[2di2\|2di2]]</td></tr>
			<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ec7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ec7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2ec7 RCSB], [http://www.ebi.ac.uk/pdbsum/2ec7 PDBsum]</span></td></tr>
			<table>
			== Evolutionary Conservation ==
			[[Image:Consurf_key_small.gif\|200px\|right]]
			Check<jmol>
			<jmolCheckbox>
			<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ec/2ec7_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The nucleocapsid (NC) protein of HIV, which contains two CCHC-type zinc fingers connected by a linker, is a multifunctional protein involved in many of the critical steps of the HIV life cycle. HIV-1 and HIV-2 contain NC proteins NCp7 and NCp8, respectively. The amino acid sequences of both NC proteins are 67% identical. For NCp7, the important elements for RNA binding were found to be the first zinc finger flanked by the linker, as the minimal active domain, and the 3(10) helix in the N-terminus, as the secondary active domain. However, for the NCp8 counterpart in HIV-2, the mechanism for binding to viral RNA has not yet been clarified. In this study, we determined NCp8's three-dimensional structure for the first time and examined the dynamic behavior and chemical shift perturbation as a function of the concentration of viral RNA SL3. Moreover, the specific binding activities of NCp8 and the NCp8-derived peptides with SL3 were examined by a native polyacrylamide gel electrophoresis assay. These results indicate that the RNA recognition mechanism for NCp8 is different from that of NCp7 and that the hydrophobic cleft in the second zinc finger acts as a secondary active domain instead of the 3(10) helix in NCp7. Furthermore, the flexibility of the linker is limited by the hydrogen bond between the first zinc finger (Asn11) and the linker (Arg27), which makes it possible for the sites around Trp10 in the minimal active domain and the secondary active domain to form the binding surface.

	~~{{STRUCTURE_2ec7\| PDB=2ec7 \| SCENE= }}~~		The RNA recognition mechanism of human immunodeficiency virus (HIV) type 2 NCp8 is different from that of HIV-1 NCp7.,Matsui T, Tanaka T, Endoh H, Sato K, Tanaka H, Miyauchi E, Kawashima Y, Nagai-Makabe M, Komatsu H, Kohno T, Maeda T, Kodera Y Biochemistry. 2009 May 26;48(20):4314-23. PMID:19334676<ref>PMID:19334676</ref>

	~~===Solution Structure~~ of ~~Human Immunodificiency Virus Type-2 Nucleocapsid Protein===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_19334676}}~~

	~~==About this Structure==~~
	~~[[2ec7]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Human_immunodeficiency_virus_type_2_(isolate_ghana-1) Human immunodeficiency virus type 2 (isolate ghana-1)]~~. ~~Full experimental information is available from [http://oca.weizmann.ac.il~~/~~oca-bin/ocashort?id=2EC7 OCA].~~

	==See Also==		==See Also==
	*[[Gag polyprotein\|Gag polyprotein]]		*[[Gag polyprotein\|Gag polyprotein]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:019334676<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Endoh, H.]]		[[Category: Endoh, H.]]
	[[Category: Kodera, Y.]]		[[Category: Kodera, Y.]]

OCA at 09:44, 20 October 2012

2012-10-20T09:44:52Z

← Older revision		Revision as of 09:44, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[2ec7]] is a 1 chain structure ~~of [[Gag polyprotein]]~~ with sequence from [http://en.wikipedia.org/wiki/~~Viruses Viruses~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EC7 OCA].		[[2ec7]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_type_2_(isolate_ghana-1) Human immunodeficiency virus type 2 (isolate ghana-1)]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2EC7 OCA].

	==See Also==		==See Also==
Line 15:		Line 15:
	==Reference==		==Reference==
	<ref group="xtra">PMID:019334676</ref><references group="xtra"/>		<ref group="xtra">PMID:019334676</ref><references group="xtra"/>
	~~[[Category: Viruses]]~~
	[[Category: Endoh, H.]]		[[Category: Endoh, H.]]
	[[Category: Kodera, Y.]]		[[Category: Kodera, Y.]]

OCA: Protected "2ec7" [edit=sysop:move=sysop]

2012-07-25T23:50:09Z

Protected "2ec7" [edit=sysop:move=sysop]

← Older revision	Revision as of 23:50, 25 July 2012
(No difference)