3dph - Revision history

OCA at 12:50, 30 August 2023

2023-08-30T12:50:46Z

← Older revision		Revision as of 12:50, 30 August 2023
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	<StructureSection load='3dph' size='340' side='right'caption='[[3dph]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='3dph' size='340' side='right'caption='[[3dph]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dph]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/~~9hiv1 9hiv1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DPH FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dph]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DPH FirstGlance]. <br>
	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[3ds4\|3ds4]], [[3ds2\|3ds2]], [[3ds3\|3ds3]], [[3dtj\|3dtj]], [[3ds1\|3ds1]], [[3ds5\|3ds5]], [[3ds0\|3ds0]]</div></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]] 2.01Å</td></tr>
	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">gag ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=11676 9HIV1])~~</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=3dph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dph OCA], [https://pdbe.org/3dph PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dph RCSB], [https://www.ebi.ac.uk/pdbsum/3dph PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dph 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=3dph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dph OCA], [https://pdbe.org/3dph PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dph RCSB], [https://www.ebi.ac.uk/pdbsum/3dph PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dph ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/~~Q72497_9HIV1 Q72497_9HIV1]~~] 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).~~[SAAS:SAAS012344_004_011858]~~		[https://www.uniprot.org/uniprot/POL_HV1N5 POL_HV1N5] Gag-Pol polyprotein and Gag polyprotein may regulate their own translation, by the binding genomic RNA in the 5'-UTR. At low concentration, Gag-Pol and Gag would promote translation, whereas at high concentration, the polyproteins encapsidate genomic RNA and then shutt off translation (By similarity). Matrix protein p17 has two main functions: in infected cell, it targets Gag and Gag-pol polyproteins to the plasma membrane via a multipartite membrane-binding signal, that includes its myristoylated N-terminus. The second function is to play a role in nuclear localization of the viral genome at the very start of cell infection. Matrix protein is the part of the pre-integration complex. It binds in the cytoplasm the human BAF protein which prevent autointegration of the viral genome, and might be included in virions at the ration of zero to 3 BAF dimer per virion. The myristoylation signal and the NLS thus exert conflicting influences its subcellular localization. The key regulation of these motifs might be phosphorylation of a portion of MA molecules on the C-terminal tyrosine at the time of virus maturation, by virion-associated cellular tyrosine kinase. Implicated in the release from host cell mediated by Vpu (By similarity). Capsid protein p24 forms the conical core that encapsulates the genomic RNA-nucleocapsid complex in the virion. Most core are conical, with only 7% tubular. The core is constituted by capsid protein hexamer subunits. The core is disassembled soon after virion entry. Interaction with human PPIA/CYPA protects the virus from restriction by human TRIM5-alpha and from an unknown antiviral activity in human cells. This capsid restriction by TRIM5 is one of the factors which restricts HIV-1 to the human species (By similarity). Nucleocapsid protein p7 encapsulates and protects viral dimeric unspliced (genomic) RNA. Binds these RNAs through its zinc fingers. Facilitates rearangement of nucleic acid secondary structure during retrotranscription of genomic RNA. This capability is referred to as nucleic acid chaperone activity (By similarity). The aspartyl protease mediates proteolytic cleavages of Gag and Gag-Pol polyproteins during or shortly after the release of the virion from the plasma membrane. Cleavages take place as an ordered, step-wise cascade to yield mature proteins. This process is called maturation. Displays maximal activity during the budding process just prior to particle release from the cell. Also cleaves Nef and Vif, probably concomitantly with viral structural proteins on maturation of virus particles (By similarity). Reverse transcriptase/ribonuclease H (RT) is a multifunctional enzyme that converts the viral RNA genome into dsDNA in the cytoplasm, shortly after virus entry into the cell. This enzyme displays a DNA polymerase activity that can copy either DNA or RNA templates, and a ribonuclease H (RNase H) activity that cleaves the RNA strand of RNA-DNA heteroduplexes in a partially processive 3' to 5' endonucleasic mode. Conversion of viral genomic RNA into dsDNA requires many steps. A tRNA(3)-Lys binds to the primer-binding site (PBS) situated at the 5'-end of the viral RNA. RT uses the 3' end of the tRNA primer to perform a short round of RNA-dependent minus-strand DNA synthesis. The reading proceeds through the U5 region and ends after the repeated (R) region which is present at both ends of viral RNA. The portion of the RNA-DNA heteroduplex is digested by the RNase H, resulting in a ssDNA product attached to the tRNA primer. This ssDNA/tRNA hybridizes with the identical R region situated at the 3' end of viral RNA. This template exchange, known as minus-strand DNA strong stop transfer, can be either intra- or intermolecular. RT uses the 3' end of this newly synthesized short ssDNA to perform the RNA-dependent minus-strand DNA synthesis of the whole template. RNase H digests the RNA template except for two polypurine tracts (PPTs) situated at the 5'-end and near the center of the genome. It is not clear if both polymerase and RNase H activities are simultaneous. RNase H probably can proceed both in a polymerase-dependent (RNA cut into small fragments by the same RT performing DNA synthesis) and a polymerase-independent mode (cleavage of remaining RNA fragments by free RTs). Secondly, RT performs DNA-directed plus-strand DNA synthesis using the PPTs that have not been removed by RNase H as primers. PPTs and tRNA primers are then removed by RNase H. The 3' and 5' ssDNA PBS regions hybridize to form a circular dsDNA intermediate. Strand displacement synthesis by RT to the PBS and PPT ends produces a blunt ended, linear dsDNA copy of the viral genome that includes long terminal repeats (LTRs) at both ends (By similarity). Integrase catalyzes viral DNA integration into the host chromosome, by performing a series of DNA cutting and joining reactions. This enzyme activity takes place after virion entry into a cell and reverse transcription of the RNA genome in dsDNA. The first step in the integration process is 3' processing. This step requires a complex comprising the viral genome, matrix protein, Vpr and integrase. This complex is called the pre-integration complex (PIC). The integrase protein removes 2 nucleotides from each 3' end of the viral DNA, leaving recessed CA OH's at the 3' ends. In the second step, the PIC enters cell nucleus. This process is mediated through integrase and Vpr proteins, and allows the virus to infect a non dividing cell. This ability to enter the nucleus is specific of lentiviruses, other retroviruses cannot and rely on cell division to access cell chromosomes. In the third step, termed strand transfer, the integrase protein joins the previously processed 3' ends to the 5' ends of strands of target cellular DNA at the site of integration. The 5'-ends are produced by integrase-catalyzed staggered cuts, 5 bp apart. A Y-shaped, gapped, recombination intermediate results, with the 5'-ends of the viral DNA strands and the 3' ends of target DNA strands remaining unjoined, flanking a gap of 5 bp. The last step is viral DNA integration into host chromosome. This involves host DNA repair synthesis in which the 5 bp gaps between the unjoined strands are filled in and then ligated. Since this process occurs at both cuts flanking the HIV genome, a 5 bp duplication of host DNA is produced at the ends of HIV-1 integration. Alternatively, Integrase may catalyze the excision of viral DNA just after strand transfer, this is termed disintegration (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: Human immunodeficiency virus 1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Igonet, S]]		[[Category: Igonet S]]
	[[Category: Rey~~, F A~~]]		[[Category: Rey FA]]
	[[Category: Vaney~~, M C]]~~		[[Category: Vaney MC]]
	~~[[Category: Assembly]]~~
	~~[[Category: Capsid]]~~
	~~[[Category: Capsid maturation]]~~
	~~[[Category: Capsid protein]]~~
	~~[[Category: Hiv]]~~
	~~[[Category: Mainly alpha]]~~
	~~[[Category: Mutant]]~~
	~~[[Category: Polyprotein]]~~
	~~[[Category: Viral protein~~]]

OCA at 19:26, 20 October 2021

2021-10-20T19:26:25Z

← Older revision		Revision as of 19:26, 20 October 2021
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	==HIV-1 capsid C-terminal domain mutant (L211S)==		==HIV-1 capsid C-terminal domain mutant (L211S)==
	<StructureSection load='3dph' size='340' side='right' caption='[[3dph]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='3dph' size='340' side='right'caption='[[3dph]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dph]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/9hiv1 9hiv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPH OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3DPH FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dph]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/9hiv1 9hiv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DPH FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ds4\|3ds4]], [[3ds2\|3ds2]], [[3ds3\|3ds3]], [[3dtj\|3dtj]], [[3ds1\|3ds1]], [[3ds5\|3ds5]], [[3ds0\|3ds0]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ds4\|3ds4]], [[3ds2\|3ds2]], [[3ds3\|3ds3]], [[3dtj\|3dtj]], [[3ds1\|3ds1]], [[3ds5\|3ds5]], [[3ds0\|3ds0]]</div></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=11676 9HIV1])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gag ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=11676 9HIV1])</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=3dph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dph OCA], [~~http~~://pdbe.org/3dph PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3dph RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3dph PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3dph 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=3dph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dph OCA], [https://pdbe.org/3dph PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dph RCSB], [https://www.ebi.ac.uk/pdbsum/3dph PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dph ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/Q72497_9HIV1 Q72497_9HIV1]] 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).[SAAS:SAAS012344_004_011858]		[[https://www.uniprot.org/uniprot/Q72497_9HIV1 Q72497_9HIV1]] 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).[SAAS:SAAS012344_004_011858]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dp/3dph_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dp/3dph_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>
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	</div>		</div>
	<div class="pdbe-citations 3dph" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3dph" 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: Large Structures]]
	[[Category: Igonet, S]]		[[Category: Igonet, S]]
	[[Category: Rey, F A]]		[[Category: Rey, F A]]

OCA at 08:54, 25 October 2017

2017-10-25T08:54:37Z

← Older revision		Revision as of 08:54, 25 October 2017
Line 1:		Line 1:

	==HIV-1 capsid C-terminal domain mutant (L211S)==		==HIV-1 capsid C-terminal domain mutant (L211S)==
	<StructureSection load='3dph' size='340' side='right' caption='[[3dph]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='3dph' size='340' side='right' caption='[[3dph]], [[Resolution\|resolution]] 2.01Å' scene=''>
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	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ds4\|3ds4]], [[3ds2\|3ds2]], [[3ds3\|3ds3]], [[3dtj\|3dtj]], [[3ds1\|3ds1]], [[3ds5\|3ds5]], [[3ds0\|3ds0]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ds4\|3ds4]], [[3ds2\|3ds2]], [[3ds3\|3ds3]], [[3dtj\|3dtj]], [[3ds1\|3ds1]], [[3ds5\|3ds5]], [[3ds0\|3ds0]]</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=11676 9HIV1])</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=11676 9HIV1])</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=3dph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dph OCA], [http://pdbe.org/3dph PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dph RCSB], [http://www.ebi.ac.uk/pdbsum/3dph 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=3dph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dph OCA], [http://pdbe.org/3dph PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dph RCSB], [http://www.ebi.ac.uk/pdbsum/3dph PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3dph ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 3dph" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 3dph" style="background-color:#fffaf0;"></div>

	~~==See Also==~~
	*[[Virus coat protein\|Virus coat protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 19:27, 9 February 2016

2016-02-09T19:27:28Z

← Older revision		Revision as of 19:27, 9 February 2016
Line 2:		Line 2:
	<StructureSection load='3dph' size='340' side='right' caption='[[3dph]], [[Resolution\|resolution]] 2.01Å' scene=''>		<StructureSection load='3dph' size='340' side='right' caption='[[3dph]], [[Resolution\|resolution]] 2.01Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dph]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Human_immunodeficiency_virus_1 Human immunodeficiency virus 1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DPH FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dph]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/9hiv1 9hiv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DPH FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ds4\|3ds4]], [[3ds2\|3ds2]], [[3ds3\|3ds3]], [[3dtj\|3dtj]], [[3ds1\|3ds1]], [[3ds5\|3ds5]], [[3ds0\|3ds0]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ds4\|3ds4]], [[3ds2\|3ds2]], [[3ds3\|3ds3]], [[3dtj\|3dtj]], [[3ds1\|3ds1]], [[3ds5\|3ds5]], [[3ds0\|3ds0]]</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=11676 ~~Human immunodeficiency virus 1~~])</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=11676 9HIV1])</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=3dph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dph OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dph RCSB], [http://www.ebi.ac.uk/pdbsum/3dph 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=3dph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dph OCA], [http://pdbe.org/3dph PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3dph RCSB], [http://www.ebi.ac.uk/pdbsum/3dph PDBsum]</span></td></tr>
	</table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/Q72497_9HIV1 Q72497_9HIV1]] 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).[SAAS:SAAS012344_004_011858]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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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=3dph ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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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 3dph" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Human immunodeficiency virus 1]]~~
	[[Category: Igonet, S]]		[[Category: Igonet, S]]
	[[Category: Rey, F A]]		[[Category: Rey, F A]]

OCA at 11:47, 20 January 2015

2015-01-20T11:47:31Z

← Older revision		Revision as of 11:47, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3dph]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DPH FirstGlance]. <br>		<table><tr><td colspan='2'>[[3dph]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DPH FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ds4\|3ds4]], [[3ds2\|3ds2]], [[3ds3\|3ds3]], [[3dtj\|3dtj]], [[3ds1\|3ds1]], [[3ds5\|3ds5]], [[3ds0\|3ds0]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ds4\|3ds4]], [[3ds2\|3ds2]], [[3ds3\|3ds3]], [[3dtj\|3dtj]], [[3ds1\|3ds1]], [[3ds5\|3ds5]], [[3ds0\|3ds0]]</td></tr>
	<tr><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=11676 Human immunodeficiency virus 1])</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=11676 Human immunodeficiency virus 1])</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=3dph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dph OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dph RCSB], [http://www.ebi.ac.uk/pdbsum/3dph 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=3dph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dph OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dph RCSB], [http://www.ebi.ac.uk/pdbsum/3dph 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 33:		Line 33:
	</StructureSection>		</StructureSection>
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
	[[Category: Igonet, S.]]		[[Category: Igonet, S]]
	[[Category: Rey, F A.]]		[[Category: Rey, F A]]
	[[Category: Vaney, M C.]]		[[Category: Vaney, M C]]
	[[Category: Assembly]]		[[Category: Assembly]]
	[[Category: Capsid]]		[[Category: Capsid]]

OCA at 13:33, 29 September 2014

2014-09-29T13:33:06Z

← Older revision		Revision as of 13:33, 29 September 2014
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	[[Image:~~3dph~~.~~png~~\|~~left~~\|~~200px~~]]		==HIV-1 capsid C-terminal domain mutant (L211S)==
			<StructureSection load='3dph' size='340' side='right' caption='[[3dph]], [[Resolution\|resolution]] 2.01Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3dph]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3DPH FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ds4\|3ds4]], [[3ds2\|3ds2]], [[3ds3\|3ds3]], [[3dtj\|3dtj]], [[3ds1\|3ds1]], [[3ds5\|3ds5]], [[3ds0\|3ds0]]</td></tr>
			<tr><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=11676 Human immunodeficiency virus 1])</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=3dph FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dph OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3dph RCSB], [http://www.ebi.ac.uk/pdbsum/3dph 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/dp/3dph_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 ==
			Morphogenesis of infectious HIV-1 involves budding of immature virions followed by proteolytic disassembly of the Gag protein shell and subsequent assembly of processed capsid proteins (CA) into the mature HIV-1 core. The dimeric interface between C-terminal domains of CA (C-CA) has been shown to be important for both immature and mature assemblies. We previously reported a CA-binding peptide (CAI) that blocks both assembly steps in vitro. The three-dimensional structure of the C-CA/CAI complex revealed an allosteric effect of CAI that alters the C-CA dimer interface. Based on this structure, we now investigated the phenotypes of mutations in the binding pocket. CA variants carrying mutations Y169A, L211A, or L211S had a reduced affinity for CAI and were unable to form mature-like particles in vitro. These mutations also blocked morphological conversion to mature virions in tissue culture and abolished infectivity. X-ray crystallographic analyses of the variant C-CA domains revealed that these alterations induced the same allosteric change at the dimer interface observed in the C-CA/CAI complex. These results point to a role of key interactions between conserved amino acids in the CAI binding pocket of C-CA in maintaining the correct conformation necessary for mature core assembly.

	~~{{STRUCTURE_3dph\| PDB=3dph \| SCENE= }}~~		Residues in the HIV-1 capsid assembly inhibitor binding site are essential for maintaining the assembly-competent quaternary structure of the capsid protein.,Bartonova V, Igonet S, Sticht J, Glass B, Habermann A, Vaney MC, Sehr P, Lewis J, Rey FA, Krausslich HG J Biol Chem. 2008 Nov 14;283(46):32024-33. Epub 2008 Sep 4. PMID:18772135<ref>PMID:18772135</ref>

	~~===HIV-1 capsid C-terminal domain mutant (L211S)===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_18772135}}~~

	~~==About this Structure==~~
	~~[[3dph]] is~~ a ~~2 chain structure with sequence from [http://en.wikipedia~~.~~org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann.ac.il/oca-bin~~/~~ocashort?id=3DPH OCA].~~

	==See Also==		==See Also==
	*[[Virus coat protein\|Virus coat protein]]		*[[Virus coat protein\|Virus coat protein]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:018772135<~~/~~ref~~><~~ref group="xtra">PMID:016041386</ref><references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
	[[Category: Igonet, S.]]		[[Category: Igonet, S.]]

OCA at 14:53, 20 October 2012

2012-10-20T14:53:30Z

← Older revision		Revision as of 14:53, 20 October 2012
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	[[Image:3dph.png\|left\|200px]]		[[Image:3dph.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3dph", creates the "Structure Box" on the page.~~
	~~You may change the PDB parameter (which sets the PDB file loaded into the applet)~~
	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~
	~~or leave the SCENE parameter empty for the default display.~~
	~~-->~~
	{{STRUCTURE_3dph\| PDB=3dph \| SCENE= }}		{{STRUCTURE_3dph\| PDB=3dph \| SCENE= }}

	===HIV-1 capsid C-terminal domain mutant (L211S)===		===HIV-1 capsid C-terminal domain mutant (L211S)===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_18772135}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 18772135 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_18772135}}		{{ABSTRACT_PUBMED_18772135}}

	==About this Structure==		==About this Structure==
	[[3dph]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPH OCA].		[[3dph]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPH OCA].

			==See Also==
			*[[Virus coat protein\|Virus coat protein]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~18772135~~</ref><ref group="xtra">PMID:~~16041386~~</ref><references group="xtra"/>		<ref group="xtra">PMID:018772135</ref><ref group="xtra">PMID:016041386</ref><references group="xtra"/>
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
	[[Category: Igonet, S.]]		[[Category: Igonet, S.]]

OCA: Protected "3dph" [edit=sysop:move=sysop]

2011-03-15T00:32:24Z

Protected "3dph" [edit=sysop:move=sysop]

← Older revision	Revision as of 00:32, 15 March 2011
(No difference)

OCA at 00:32, 15 March 2011

2011-03-15T00:32:22Z

← Older revision		Revision as of 00:32, 15 March 2011
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	~~{{Seed}}~~
	[[Image:3dph.png\|left\|200px]]		[[Image:3dph.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
	~~3DPH~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPH OCA].		[[3dph]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human_immunodeficiency_virus_1 Human immunodeficiency virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DPH OCA].

	==Reference==		==Reference==
Line 37:		Line 36:
	[[Category: Polyprotein]]		[[Category: Polyprotein]]
	[[Category: Viral protein]]		[[Category: Viral protein]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:12:10 2009''~~

OCA at 10:12, 17 February 2009

2009-02-17T10:12:11Z

← Older revision		Revision as of 10:12, 17 February 2009
Line 23:		Line 23:

	==Reference==		==Reference==
	Residues in the HIV-1 Capsid Assembly Inhibitor Binding Site Are Essential for Maintaining the Assembly-competent Quaternary Structure of the Capsid Protein., Bartonova V, Igonet S, Sticht J, Glass B, Habermann A, Vaney MC, Sehr P, Lewis J, Rey FA, Krausslich HG, J Biol Chem. 2008 Nov 14;283(46):32024-33. Epub 2008 Sep 4. PMID:~~[http://www.ncbi.nlm.nih.gov/pubmed~~/~~18772135 18772135]~~		<ref group="xtra">PMID:18772135</ref><ref group="xtra">PMID:16041386</ref><references group="xtra"/>

	The HIV-1 capsid protein C-terminal domain in complex with a virus assembly inhibitor., Ternois F, Sticht J, Duquerroy S, Krausslich HG, Rey FA, Nat Struct Mol Biol. 2005 Aug;12(8):678-82. Epub 2005 Jul 24. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/16041386 16041386]~~
	[[Category: Human immunodeficiency virus 1]]		[[Category: Human immunodeficiency virus 1]]
	[[Category: Igonet, S.]]		[[Category: Igonet, S.]]
Line 40:		Line 38:
	[[Category: Viral protein]]		[[Category: Viral protein]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Nov 27 13~~:52:~~37 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 12:12:10 2009''