3lry - Revision history

OCA at 08:43, 6 September 2023

OCA — Wed, 06 Sep 2023 08:43:08 GMT

←Older revision		Revision as of 08:43, 6 September 2023
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	<StructureSection load='3lry' size='340' side='right'caption='[[3lry]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='3lry' size='340' side='right'caption='[[3lry]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lry]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LRY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3LRY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lry]] 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=3LRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LRY FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[1a43\|1a43]]~~, [[~~3ds5~~\|~~3ds5]], [[3dtj\|3dtj~~]]</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]] 1.98Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=3lry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lry OCA], [~~http~~://pdbe.org/3lry PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3lry RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3lry PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3lry 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=3lry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lry OCA], [https://pdbe.org/3lry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lry RCSB], [https://www.ebi.ac.uk/pdbsum/3lry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lry ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[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: Lu, W]]	+	[[Category: Lu W]]
-	[[Category: Pazgier, M]]	+	[[Category: Pazgier M]]
-	~~[[Category: Aid]]~~	+
-	~~[[Category: C-terminal domain]]~~	+
-	~~[[Category: Core protein]]~~	+
-	~~[[Category: Hiv]]~~	+
-	~~[[Category: Hiv-1 capsid]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 06:37, 14 October 2020

OCA — Wed, 14 Oct 2020 06:37:22 GMT

←Older revision		Revision as of 06:37, 14 October 2020
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	==Crystal structure of synthetic HIV-1 capsid C-terminal domain (CCA)==		==Crystal structure of synthetic HIV-1 capsid C-terminal domain (CCA)==
-	<StructureSection load='3lry' size='340' side='right' caption='[[3lry]], [[Resolution\|resolution]] 1.98Å' scene=''>	+	<StructureSection load='3lry' size='340' side='right'caption='[[3lry]], [[Resolution\|resolution]] 1.98Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3lry]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LRY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3LRY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3lry]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LRY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3LRY FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a43\|1a43]], [[3ds5\|3ds5]], [[3dtj\|3dtj]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a43\|1a43]], [[3ds5\|3ds5]], [[3dtj\|3dtj]]</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=3lry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lry OCA], [http://pdbe.org/3lry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lry RCSB], [http://www.ebi.ac.uk/pdbsum/3lry PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lry ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3lry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lry OCA], [http://pdbe.org/3lry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lry RCSB], [http://www.ebi.ac.uk/pdbsum/3lry PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lry ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 28:		Line 28:

	==See Also==		==See Also==
-	*[[Virus coat ~~protein~~\|Virus coat ~~protein~~]]	+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Lu, W]]		[[Category: Lu, W]]
	[[Category: Pazgier, M]]		[[Category: Pazgier, M]]

OCA at 07:36, 9 January 2019

OCA — Wed, 09 Jan 2019 07:36:35 GMT

←Older revision		Revision as of 07:36, 9 January 2019
Line 1:		Line 1:
		+
	==Crystal structure of synthetic HIV-1 capsid C-terminal domain (CCA)==		==Crystal structure of synthetic HIV-1 capsid C-terminal domain (CCA)==
	<StructureSection load='3lry' size='340' side='right' caption='[[3lry]], [[Resolution\|resolution]] 1.98Å' scene=''>		<StructureSection load='3lry' size='340' side='right' caption='[[3lry]], [[Resolution\|resolution]] 1.98Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[3lry]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LRY FirstGlance]. <br>		<table><tr><td colspan='2'>[[3lry]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LRY FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a43\|1a43]], [[3ds5\|3ds5]], [[3dtj\|3dtj]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a43\|1a43]], [[3ds5\|3ds5]], [[3dtj\|3dtj]]</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=3lry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lry OCA], [http://pdbe.org/3lry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lry RCSB], [http://www.ebi.ac.uk/pdbsum/3lry 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=3lry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lry OCA], [http://pdbe.org/3lry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lry RCSB], [http://www.ebi.ac.uk/pdbsum/3lry PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3lry ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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/lr/3lry_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lr/3lry_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 00:02, 9 February 2016

OCA — Tue, 09 Feb 2016 00:02:23 GMT

←Older revision		Revision as of 00:02, 9 February 2016
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	<table><tr><td colspan='2'>[[3lry]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LRY FirstGlance]. <br>		<table><tr><td colspan='2'>[[3lry]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LRY FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a43\|1a43]], [[3ds5\|3ds5]], [[3dtj\|3dtj]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a43\|1a43]], [[3ds5\|3ds5]], [[3dtj\|3dtj]]</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=3lry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lry RCSB], [http://www.ebi.ac.uk/pdbsum/3lry 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=3lry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lry OCA], [http://pdbe.org/3lry PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3lry RCSB], [http://www.ebi.ac.uk/pdbsum/3lry PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 14:		Line 14:
	<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=3lry 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 3lry" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 08:32, 20 January 2015

OCA — Tue, 20 Jan 2015 08:32:13 GMT

←Older revision		Revision as of 08:32, 20 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3lry]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LRY FirstGlance]. <br>		<table><tr><td colspan='2'>[[3lry]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LRY FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a43\|1a43]], [[3ds5\|3ds5]], [[3dtj\|3dtj]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a43\|1a43]], [[3ds5\|3ds5]], [[3dtj\|3dtj]]</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=3lry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lry RCSB], [http://www.ebi.ac.uk/pdbsum/3lry 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=3lry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lry RCSB], [http://www.ebi.ac.uk/pdbsum/3lry PDBsum]</span></td></tr>
-	<table>	+	</table>
	== 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: Lu, W.]]	+	[[Category: Lu, W]]
-	[[Category: Pazgier, M.]]	+	[[Category: Pazgier, M]]
	[[Category: Aid]]		[[Category: Aid]]
	[[Category: C-terminal domain]]		[[Category: C-terminal domain]]

OCA at 11:17, 29 September 2014

OCA — Mon, 29 Sep 2014 11:17:03 GMT

←Older revision		Revision as of 11:17, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~3lry.~~png~~\|~~left~~\|200px]]	+	==Crystal structure of synthetic HIV-1 capsid C-terminal domain (CCA)==
		+	<StructureSection load='3lry' size='340' side='right' caption='[[3lry]], [[Resolution\|resolution]] 1.98Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3lry]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LRY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3LRY FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1a43\|1a43]], [[3ds5\|3ds5]], [[3dtj\|3dtj]]</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=3lry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lry OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3lry RCSB], [http://www.ebi.ac.uk/pdbsum/3lry 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/lr/3lry_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 ==
		+	A retro-inverso peptide is made up of d-amino acids in a reversed sequence and, when extended, assumes a side chain topology similar to that of its parent molecule but with inverted amide peptide bonds. Despite their limited success as antigenic mimicry, retro-inverso isomers generally fail to emulate the protein-binding activities of their parent peptides of an alpha-helical nature. In studying the interaction between the tumor suppressor protein p53 and its negative regulator MDM2, Sakurai et al. (Sakurai, K., Chung, H. S., and Kahne, D. (2004) J. Am. Chem. Soc. 126, 16288-16289) made a surprising finding that the retro-inverso isomer of p53(15-29) retained the same binding activity as the wild type peptide as determined by inhibition enzyme-linked immunosorbent assay. The authors attributed the unusual outcome to the ability of the D-peptide to adopt a right-handed helical conformation upon MDM2 binding. Using a battery of biochemical and biophysical tools, we found that retro-inverso isomerization diminished p53 (15-29) binding to MDM2 or MDMX by 3.2-3.3 kcal/mol. Similar results were replicated with the C-terminal domain of HIV-1 capsid protein (3.0 kcal/mol) and the Src homology 3 domain of Abl tyrosine kinase (3.4 kcal/mol). CD and NMR spectroscopic as well as x-ray crystallographic studies showed that D-peptide ligands of MDM2 invariably adopted left-handed helical conformations in both free and bound states. Our findings reinforce that the retro-inverso strategy works poorly in molecular mimicry of biologically active helical peptides, due to inherent differences at the secondary and tertiary structure levels between an l-peptide and its retro-inverso isomer despite their similar side chain topologies at the primary structure level.

-	~~{{STRUCTURE_3lry\| PDB=3lry \| SCENE= }}~~	+	Limitations of peptide retro-inverso isomerization in molecular mimicry.,Li C, Pazgier M, Li J, Li C, Liu M, Zou G, Li Z, Chen J, Tarasov SG, Lu WY, Lu W J Biol Chem. 2010 Jun 18;285(25):19572-81. Epub 2010 Apr 9. PMID:20382735<ref>PMID:20382735</ref>

-	~~===Crystal structure~~ of ~~synthetic HIV-1 capsid C-terminal domain (CCA)===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_20382735}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3lry]] is a 2 chain structure~~. ~~Full crystallographic information is available from [http://oca~~.~~weizmann~~.~~ac.il~~/~~oca-bin/ocashort?id=3LRY OCA].~~	+

	==See Also==		==See Also==
	*[[Virus coat protein\|Virus coat protein]]		*[[Virus coat protein\|Virus coat protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:020382735<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Lu, W.]]		[[Category: Lu, W.]]
	[[Category: Pazgier, M.]]		[[Category: Pazgier, M.]]

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

OCA — Sat, 20 Oct 2012 11:55:55 GMT

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

←Older revision

Revision as of 11:55, 20 October 2012

OCA at 11:55, 20 October 2012

OCA — Sat, 20 Oct 2012 11:55:53 GMT

←Older revision		Revision as of 11:55, 20 October 2012
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-	{{Seed}}
	[[Image:3lry.png\|left\|200px]]		[[Image:3lry.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_3lry", 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_3lry\| PDB=3lry \| SCENE= }}		{{STRUCTURE_3lry\| PDB=3lry \| SCENE= }}

	===Crystal structure of synthetic HIV-1 capsid C-terminal domain (CCA)===		===Crystal structure of synthetic HIV-1 capsid C-terminal domain (CCA)===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_20382735}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 20382735 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_20382735}}		{{ABSTRACT_PUBMED_20382735}}

	==About this Structure==		==About this Structure==
-	~~3LRY~~ is a 2 ~~chains~~ structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LRY OCA].	+	[[3lry]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LRY OCA].
		+
		+	==See Also==
		+	*[[Virus coat protein\|Virus coat protein]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~20382735~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:020382735</ref><references group="xtra"/>
	[[Category: Lu, W.]]		[[Category: Lu, W.]]
	[[Category: Pazgier, M.]]		[[Category: Pazgier, M.]]
Line 32:		Line 23:
	[[Category: Hiv-1 capsid]]		[[Category: Hiv-1 capsid]]
	[[Category: Viral protein]]		[[Category: Viral protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 28 10:44:23 2010''

OCA at 07:44, 28 April 2010

OCA — Wed, 28 Apr 2010 07:44:25 GMT

←Older revision		Revision as of 07:44, 28 April 2010
Line 1:		Line 1:
	{{Seed}}		{{Seed}}
-	[[Image:3lry.~~jpg~~\|left\|200px]]	+	[[Image:3lry.png\|left\|200px]]

	<!--		<!--
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	===Crystal structure of synthetic HIV-1 capsid C-terminal domain (CCA)===		===Crystal structure of synthetic HIV-1 capsid C-terminal domain (CCA)===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_20382735}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 20382735 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_20382735}}

	==About this Structure==		==About this Structure==
	3LRY is a 2 chains structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LRY OCA].		3LRY is a 2 chains structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LRY OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:20382735</ref><references group="xtra"/>
	[[Category: Lu, W.]]		[[Category: Lu, W.]]
	[[Category: Pazgier, M.]]		[[Category: Pazgier, M.]]
Line 24:		Line 33:
	[[Category: Viral protein]]		[[Category: Viral protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar~~ 10 ~~14:49~~:44 2010''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 28 10:44:23 2010''

OCA at 12:49, 10 March 2010

OCA — Wed, 10 Mar 2010 12:49:46 GMT

←Older revision		Revision as of 12:49, 10 March 2010
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3lry.jpg\|left\|200px]]

-	The ~~entry 3lry~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3lry", 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_3lry\| PDB=3lry \| SCENE= }}

-	~~Authors: Pazgier, M., Lu, W.~~	+	===Crystal structure of synthetic HIV-1 capsid C-terminal domain (CCA)===

-	Description: Crystal structure of synthetic HIV-1 capsid C-terminal domain (CCA)

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Thu Feb 25 13~~:04:20 2010''	+	==About this Structure==
		+	3LRY is a 2 chains structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3LRY OCA].
		+	[[Category: Lu, W.]]
		+	[[Category: Pazgier, M.]]
		+	[[Category: Aid]]
		+	[[Category: C-terminal domain]]
		+	[[Category: Core protein]]
		+	[[Category: Hiv]]
		+	[[Category: Hiv-1 capsid]]
		+	[[Category: Viral protein]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Mar 10 14:49:44 2010''