1a6b - Revision history

OCA at 08:11, 22 May 2024

2024-05-22T08:11:27Z

←Older revision		Revision as of 08:11, 22 May 2024
Line 20:		Line 20:
	</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=1a6b 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=1a6b ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The structure of the 56 amino acid nucleocapsid protein NCp10 of retrovirus MoMuLV, which contains a single CX(2)CX(4)HX(4)C-type zinc finger, has been determined previously by NMR. The important role of NCp10 (or NCp7 for HIV-1) in the retroviral life cycle seems mainly related to their preferential binding to single-stranded nucleic acids. We report here the structure of the complex formed between the biologically active (14-53)NCp10 and the oligonucleotide d(ACGCC) in aqueous solution determined by 2D (1)H NMR based methods. The aromatic residue Trp(35) of NCp10 directs nucleic acid complexation as shown by its complete fluorescence quenching upon addition of d(ACGCC). (1)H and (31)P NMR studies support the insertion of Trp(35) between the G(3) and C(4) bases. A total of 577 NOE distance restraints, of which 40 were intermolecular, were used for the structure determination. The zinc finger provides a well-defined surface for the binding of d(ACGCC) through hydrophobic interactions and tryptophan stacking on the guanine. This latter interaction was also observed in the NMR-derived structures of the complexes between NCp7, which contains two successive zinc fingers, and single-stranded DNA and RNA, supporting the proposal for a major role played by aromatic residues of NCp proteins in nucleic acid recognition. Upon binding to the nucleotide a new loop in NCp10 that participates in the intermolecular interaction is formed. Additional interactions provided by positively charged residues surrounding the zinc finger appear necessary for tight binding. The structure of the complex NCp10-d(ACGCC) gives a structural explanation for the loss of virus infectivity following point mutations in the finger domain.
		+
		+	NMR structure of the complex between the zinc finger protein NCp10 of Moloney murine leukemia virus and the single-stranded pentanucleotide d(ACGCC): comparison with HIV-NCp7 complexes.,Schuler W, Dong C, Wecker K, Roques BP Biochemistry. 1999 Oct 5;38(40):12984-94. PMID:10529168<ref>PMID:10529168</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 1a6b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 15:21, 13 March 2024

2024-03-13T15:21:42Z

←Older revision		Revision as of 15:21, 13 March 2024
Line 1:		Line 1:

	==NMR STRUCTURE OF THE COMPLEX BETWEEN THE ZINC FINGER PROTEIN NCP10 OF MOLONEY MURINE LEUKEMIA VIRUS AND A SEQUENCE OF THE PSI-PACKAGING DOMAIN OF HIV-1, 20 STRUCTURES==		==NMR STRUCTURE OF THE COMPLEX BETWEEN THE ZINC FINGER PROTEIN NCP10 OF MOLONEY MURINE LEUKEMIA VIRUS AND A SEQUENCE OF THE PSI-PACKAGING DOMAIN OF HIV-1, 20 STRUCTURES==
-	<StructureSection load='1a6b' size='340' side='right'caption='[[1a6b~~]], [[NMR_Ensembles_of_Models \| 20 NMR models~~]]' scene=''>	+	<StructureSection load='1a6b' size='340' side='right'caption='[[1a6b]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1a6b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A6B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A6B FirstGlance]. <br>		<table><tr><td colspan='2'>[[1a6b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A6B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A6B 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='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=1a6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a6b OCA], [https://pdbe.org/1a6b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a6b RCSB], [https://www.ebi.ac.uk/pdbsum/1a6b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a6b 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=1a6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a6b OCA], [https://pdbe.org/1a6b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a6b RCSB], [https://www.ebi.ac.uk/pdbsum/1a6b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a6b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/GAG_MLVMS GAG_MLVMS]] Gag polyprotein plays a role in budding and is processed by the viral protease during virion maturation outside the cell. During budding, it recruits, in a PPXY-dependent or independent manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules to Gag, or to Gag binding host factors. Interaction with HECT ubiquitin ligases probably link the viral protein to the host ESCRT pathway and facilitate release.<ref>PMID:19864377</ref> Matrix protein p15 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 (By similarity).<ref>PMID:19864377</ref> Capsid protein p30 forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex (By similarity).<ref>PMID:19864377</ref> Nucleocapsid protein p10 is involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization.<ref>PMID:19864377</ref>	+	[https://www.uniprot.org/uniprot/GAG_MLVMS GAG_MLVMS] Gag polyprotein plays a role in budding and is processed by the viral protease during virion maturation outside the cell. During budding, it recruits, in a PPXY-dependent or independent manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules to Gag, or to Gag binding host factors. Interaction with HECT ubiquitin ligases probably link the viral protein to the host ESCRT pathway and facilitate release.<ref>PMID:19864377</ref> Matrix protein p15 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 (By similarity).<ref>PMID:19864377</ref> Capsid protein p30 forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex (By similarity).<ref>PMID:19864377</ref> Nucleocapsid protein p10 is involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization.<ref>PMID:19864377</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 20:
	</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=1a6b 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=1a6b ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The structure of the 56 amino acid nucleocapsid protein NCp10 of retrovirus MoMuLV, which contains a single CX(2)CX(4)HX(4)C-type zinc finger, has been determined previously by NMR. The important role of NCp10 (or NCp7 for HIV-1) in the retroviral life cycle seems mainly related to their preferential binding to single-stranded nucleic acids. We report here the structure of the complex formed between the biologically active (14-53)NCp10 and the oligonucleotide d(ACGCC) in aqueous solution determined by 2D (1)H NMR based methods. The aromatic residue Trp(35) of NCp10 directs nucleic acid complexation as shown by its complete fluorescence quenching upon addition of d(ACGCC). (1)H and (31)P NMR studies support the insertion of Trp(35) between the G(3) and C(4) bases. A total of 577 NOE distance restraints, of which 40 were intermolecular, were used for the structure determination. The zinc finger provides a well-defined surface for the binding of d(ACGCC) through hydrophobic interactions and tryptophan stacking on the guanine. This latter interaction was also observed in the NMR-derived structures of the complexes between NCp7, which contains two successive zinc fingers, and single-stranded DNA and RNA, supporting the proposal for a major role played by aromatic residues of NCp proteins in nucleic acid recognition. Upon binding to the nucleotide a new loop in NCp10 that participates in the intermolecular interaction is formed. Additional interactions provided by positively charged residues surrounding the zinc finger appear necessary for tight binding. The structure of the complex NCp10-d(ACGCC) gives a structural explanation for the loss of virus infectivity following point mutations in the finger domain.
-
-	NMR structure of the complex between the zinc finger protein NCp10 of Moloney murine leukemia virus and the single-stranded pentanucleotide d(ACGCC): comparison with HIV-NCp7 complexes.,Schuler W, Dong C, Wecker K, Roques BP Biochemistry. 1999 Oct 5;38(40):12984-94. PMID:10529168<ref>PMID:10529168</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1a6b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 33:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Dong, C Z]]	+	[[Category: Dong C-Z]]
-	[[Category: Roques~~, B P~~]]	+	[[Category: Roques BP]]
-	[[Category: Schueler, W]]	+	[[Category: Schueler W]]
-	[[Category: Wecker, K]]	+	[[Category: Wecker K]]
-	~~[[Category: Intercalation]]~~	+
-	~~[[Category: Nucleic acid]]~~	+
-	~~[[Category: Nucleocapsid protein]]~~	+
-	~~[[Category: Retrovirus]]~~	+
-	~~[[Category: Viral protein-dna complex]]~~	+
-	~~[[Category: Zinc finger~~]]	+

OCA at 09:42, 26 May 2021

2021-05-26T09:42:44Z

←Older revision		Revision as of 09:42, 26 May 2021
Line 3:		Line 3:
	<StructureSection load='1a6b' size='340' side='right'caption='[[1a6b]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1a6b' size='340' side='right'caption='[[1a6b]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1a6b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A6B OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1A6B FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1a6b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A6B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1A6B 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='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=1a6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a6b OCA], [~~http~~://pdbe.org/1a6b PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1a6b RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1a6b PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1a6b 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=1a6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a6b OCA], [https://pdbe.org/1a6b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1a6b RCSB], [https://www.ebi.ac.uk/pdbsum/1a6b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1a6b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/GAG_MLVMS GAG_MLVMS]] Gag polyprotein plays a role in budding and is processed by the viral protease during virion maturation outside the cell. During budding, it recruits, in a PPXY-dependent or independent manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules to Gag, or to Gag binding host factors. Interaction with HECT ubiquitin ligases probably link the viral protein to the host ESCRT pathway and facilitate release.<ref>PMID:19864377</ref> Matrix protein p15 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 (By similarity).<ref>PMID:19864377</ref> Capsid protein p30 forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex (By similarity).<ref>PMID:19864377</ref> Nucleocapsid protein p10 is involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization.<ref>PMID:19864377</ref>	+	[[https://www.uniprot.org/uniprot/GAG_MLVMS GAG_MLVMS]] Gag polyprotein plays a role in budding and is processed by the viral protease during virion maturation outside the cell. During budding, it recruits, in a PPXY-dependent or independent manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules to Gag, or to Gag binding host factors. Interaction with HECT ubiquitin ligases probably link the viral protein to the host ESCRT pathway and facilitate release.<ref>PMID:19864377</ref> Matrix protein p15 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 (By similarity).<ref>PMID:19864377</ref> Capsid protein p30 forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex (By similarity).<ref>PMID:19864377</ref> Nucleocapsid protein p10 is involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization.<ref>PMID:19864377</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:03, 21 August 2019

2019-08-21T07:03:17Z

←Older revision		Revision as of 07:03, 21 August 2019
Line 1:		Line 1:

	==NMR STRUCTURE OF THE COMPLEX BETWEEN THE ZINC FINGER PROTEIN NCP10 OF MOLONEY MURINE LEUKEMIA VIRUS AND A SEQUENCE OF THE PSI-PACKAGING DOMAIN OF HIV-1, 20 STRUCTURES==		==NMR STRUCTURE OF THE COMPLEX BETWEEN THE ZINC FINGER PROTEIN NCP10 OF MOLONEY MURINE LEUKEMIA VIRUS AND A SEQUENCE OF THE PSI-PACKAGING DOMAIN OF HIV-1, 20 STRUCTURES==
-	<StructureSection load='1a6b' size='340' side='right' caption='[[1a6b]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>	+	<StructureSection load='1a6b' size='340' side='right'caption='[[1a6b]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1a6b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1A6B FirstGlance]. <br>		<table><tr><td colspan='2'>[[1a6b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1A6B FirstGlance]. <br>
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a6/1a6b_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a6/1a6b_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>
Line 32:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Dong, C Z]]		[[Category: Dong, C Z]]
	[[Category: Roques, B P]]		[[Category: Roques, B P]]

OCA at 10:32, 15 November 2017

2017-11-15T10:32:19Z

←Older revision		Revision as of 10:32, 15 November 2017
Line 1:		Line 1:
		+
	==NMR STRUCTURE OF THE COMPLEX BETWEEN THE ZINC FINGER PROTEIN NCP10 OF MOLONEY MURINE LEUKEMIA VIRUS AND A SEQUENCE OF THE PSI-PACKAGING DOMAIN OF HIV-1, 20 STRUCTURES==		==NMR STRUCTURE OF THE COMPLEX BETWEEN THE ZINC FINGER PROTEIN NCP10 OF MOLONEY MURINE LEUKEMIA VIRUS AND A SEQUENCE OF THE PSI-PACKAGING DOMAIN OF HIV-1, 20 STRUCTURES==
	<StructureSection load='1a6b' size='340' side='right' caption='[[1a6b]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>		<StructureSection load='1a6b' size='340' side='right' caption='[[1a6b]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[1a6b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1A6B FirstGlance]. <br>		<table><tr><td colspan='2'>[[1a6b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1A6B 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='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=1a6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a6b OCA], [http://pdbe.org/1a6b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1a6b RCSB], [http://www.ebi.ac.uk/pdbsum/1a6b 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=1a6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a6b OCA], [http://pdbe.org/1a6b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1a6b RCSB], [http://www.ebi.ac.uk/pdbsum/1a6b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1a6b ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 07:18, 10 February 2016

2016-02-10T07:18:36Z

←Older revision		Revision as of 07:18, 10 February 2016
Line 4:		Line 4:
	<table><tr><td colspan='2'>[[1a6b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1A6B FirstGlance]. <br>		<table><tr><td colspan='2'>[[1a6b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1A6B 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='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=1a6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a6b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1a6b RCSB], [http://www.ebi.ac.uk/pdbsum/1a6b 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=1a6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a6b OCA], [http://pdbe.org/1a6b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1a6b RCSB], [http://www.ebi.ac.uk/pdbsum/1a6b PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 16:
	<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=1a6b ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 15:37, 9 September 2015

2015-09-09T15:37:49Z

←Older revision		Revision as of 15:37, 9 September 2015
Line 26:		Line 26:
	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 1a6b" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:41, 25 December 2014

2014-12-25T12:41:09Z

←Older revision		Revision as of 12:41, 25 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=1a6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a6b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1a6b RCSB], [http://www.ebi.ac.uk/pdbsum/1a6b 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=1a6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a6b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1a6b RCSB], [http://www.ebi.ac.uk/pdbsum/1a6b PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/GAG_MLVMS GAG_MLVMS]] Gag polyprotein plays a role in budding and is processed by the viral protease during virion maturation outside the cell. During budding, it recruits, in a PPXY-dependent or independent manner, Nedd4-like ubiquitin ligases that conjugate ubiquitin molecules to Gag, or to Gag binding host factors. Interaction with HECT ubiquitin ligases probably link the viral protein to the host ESCRT pathway and facilitate release.<ref>PMID:19864377</ref> Matrix protein p15 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 (By similarity).<ref>PMID:19864377</ref> Capsid protein p30 forms the spherical core of the virion that encapsulates the genomic RNA-nucleocapsid complex (By similarity).<ref>PMID:19864377</ref> Nucleocapsid protein p10 is involved in the packaging and encapsidation of two copies of the genome. Binds with high affinity to conserved UCUG elements within the packaging signal, located near the 5'-end of the genome. This binding is dependent on genome dimerization.<ref>PMID:19864377</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 11:23, 22 December 2014

2014-12-22T11:23:33Z

←Older revision		Revision as of 11:23, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1a6b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1A6B FirstGlance]. <br>		<table><tr><td colspan='2'>[[1a6b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1A6B 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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1a6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a6b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1a6b RCSB], [http://www.ebi.ac.uk/pdbsum/1a6b 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=1a6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a6b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1a6b RCSB], [http://www.ebi.ac.uk/pdbsum/1a6b PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 28:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Dong, C Z.]]	+	[[Category: Dong, C Z]]
-	[[Category: Roques, B P.]]	+	[[Category: Roques, B P]]
-	[[Category: Schueler, W.]]	+	[[Category: Schueler, W]]
-	[[Category: Wecker, K.]]	+	[[Category: Wecker, K]]
	[[Category: Intercalation]]		[[Category: Intercalation]]
	[[Category: Nucleic acid]]		[[Category: Nucleic acid]]

OCA at 08:24, 23 July 2014

2014-07-23T08:24:32Z

←Older revision		Revision as of 08:24, 23 July 2014
Line 1:		Line 1:
-	[[~~Image~~:1a6b.~~png\|left~~\|200px]]	+	==NMR STRUCTURE OF THE COMPLEX BETWEEN THE ZINC FINGER PROTEIN NCP10 OF MOLONEY MURINE LEUKEMIA VIRUS AND A SEQUENCE OF THE PSI-PACKAGING DOMAIN OF HIV-1, 20 STRUCTURES==
		+	<StructureSection load='1a6b' size='340' side='right' caption='[[1a6b]], [[NMR_Ensembles_of_Models \| 20 NMR models]]' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1a6b]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A6B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1A6B 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>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1a6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1a6b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1a6b RCSB], [http://www.ebi.ac.uk/pdbsum/1a6b 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/a6/1a6b_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 structure of the 56 amino acid nucleocapsid protein NCp10 of retrovirus MoMuLV, which contains a single CX(2)CX(4)HX(4)C-type zinc finger, has been determined previously by NMR. The important role of NCp10 (or NCp7 for HIV-1) in the retroviral life cycle seems mainly related to their preferential binding to single-stranded nucleic acids. We report here the structure of the complex formed between the biologically active (14-53)NCp10 and the oligonucleotide d(ACGCC) in aqueous solution determined by 2D (1)H NMR based methods. The aromatic residue Trp(35) of NCp10 directs nucleic acid complexation as shown by its complete fluorescence quenching upon addition of d(ACGCC). (1)H and (31)P NMR studies support the insertion of Trp(35) between the G(3) and C(4) bases. A total of 577 NOE distance restraints, of which 40 were intermolecular, were used for the structure determination. The zinc finger provides a well-defined surface for the binding of d(ACGCC) through hydrophobic interactions and tryptophan stacking on the guanine. This latter interaction was also observed in the NMR-derived structures of the complexes between NCp7, which contains two successive zinc fingers, and single-stranded DNA and RNA, supporting the proposal for a major role played by aromatic residues of NCp proteins in nucleic acid recognition. Upon binding to the nucleotide a new loop in NCp10 that participates in the intermolecular interaction is formed. Additional interactions provided by positively charged residues surrounding the zinc finger appear necessary for tight binding. The structure of the complex NCp10-d(ACGCC) gives a structural explanation for the loss of virus infectivity following point mutations in the finger domain.

-	~~{{STRUCTURE_1a6b\| PDB=1a6b \| SCENE= }}~~	+	NMR structure of the complex between the zinc finger protein NCp10 of Moloney murine leukemia virus and the single-stranded pentanucleotide d(ACGCC): comparison with HIV-NCp7 complexes.,Schuler W, Dong C, Wecker K, Roques BP Biochemistry. 1999 Oct 5;38(40):12984-94. PMID:10529168<ref>PMID:10529168</ref>

-	~~===NMR STRUCTURE OF THE COMPLEX BETWEEN THE ZINC FINGER PROTEIN NCP10 OF MOLONEY MURINE LEUKEMIA VIRUS AND A SEQUENCE OF THE PSI-PACKAGING DOMAIN OF HIV-1~~, ~~20 STRUCTURES===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_10529168}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1a6b]] is~~ a ~~2 chain structure~~. ~~Full experimental information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=1A6B OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:010529168<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Dong, C Z.]]		[[Category: Dong, C Z.]]
	[[Category: Roques, B P.]]		[[Category: Roques, B P.]]