1j5q - Revision history

OCA: Redirecting to 5tiq

OCA — Wed, 20 Dec 2017 06:00:42 GMT

Redirecting to 5tiq

←Older revision		Revision as of 06:00, 20 December 2017
Line 1:		Line 1:
-	~~==The Structure and Evolution of the Major Capsid Protein of a Large, Lipid-containing, DNA virus.==~~	+	#REDIRECT [[5tiq]] This PDB entry is obsolete and replaced by 5tiq
-	~~<StructureSection load='1j5q' size='340' side='right' caption='~~[[~~1j5q]], [[Resolution\|resolution]] 2.55Å' scene=''>~~	+
-	~~== Structural highlights ==~~	+
-	~~<table><tr><td colspan='2'>[[1j5q~~]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Chlorella_pbcv-1_virus Chlorella pbcv-1 virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J5Q FirstGlance]. <br>	+
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr>	+
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m3y\|1m3y]], [[1m4x\|1m4x]]</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=1j5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j5q OCA], [http://pdbe.org/1j5q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j5q RCSB], [http://www.ebi.ac.uk/pdbsum/1j5q 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/j5/1j5q_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/main_output.php?pdb_ID=1j5q ConSurf].~~	+
-	~~<div style="clear:both"></div>~~	+
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Paramecium bursaria Chlorella virus type 1 (PBCV-1) is a very large, icosahedral virus containing an internal membrane enclosed within a glycoprotein coat consisting of pseudohexagonal arrays of trimeric capsomers. Each capsomer is composed of three molecules of the major capsid protein, Vp54, the 2.0-A resolution structure of which is reported here. Four N-linked and two O-linked glycosylation sites were identified. The N-linked sites are associated with nonstandard amino acid motifs as a result of glycosylation by virus-encoded enzymes. Each monomer of the trimeric structure consists of two eight-stranded, antiparallel beta-barrel, "jelly-roll" domains related by a pseudo-sixfold rotation. The fold of the monomer and the pseudo-sixfold symmetry of the capsomer resembles that of the major coat proteins in the double-stranded DNA bacteriophage PRD1 and the double-stranded DNA human adenoviruses, as well as the viral proteins VP2-VP3 of picornaviruses. The structural similarities among these diverse groups of viruses, whose hosts include bacteria, unicellular eukaryotes, plants, and mammals, make it probable that their capsid proteins have evolved from a common ancestor that had already acquired a pseudo-sixfold organization. The trimeric capsid protein structure was used to produce a quasi-atomic model of the 1,900-A diameter PBCV-1 outer shell, based on fitting of the Vp54 crystal structure into a three-dimensional cryoelectron microscopy image reconstruction of the virus.	+
-		+
-	The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus.,Nandhagopal N, Simpson AA, Gurnon JR, Yan X, Baker TS, Graves MV, Van Etten JL, Rossmann MG Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):14758-63. Epub 2002 Oct 31. PMID:12411581<ref>PMID:12411581</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 1j5q" style="background-color:#fffaf0;"></div>~~	+
-		+
-	~~==See Also==~~	+
-	*[[Virus coat protein\|Virus coat protein]]	+
-	~~== References ==~~	+
-	~~<references/>~~	+
-	~~__TOC__~~	+
-	~~</StructureSection>~~	+
-	~~[[Category: Chlorella pbcv-1 virus]]~~	+
-	~~[[Category: Baker, T S]]~~	+
-	~~[[Category: Etten, J L.Van]]~~	+
-	~~[[Category: Graves, M V]]~~	+
-	~~[[Category: Gurnon, J R]]~~	+
-	~~[[Category: Nandhagopal, N]]~~	+
-	~~[[Category: Rossmann, M G]]~~	+
-	~~[[Category: Simpson, A A]]~~	+
-	~~[[Category: Yan, X]]~~	+
-	~~[[Category: Chlorella virus]]~~	+
-	~~[[Category: Major capsid protein of large dna virus]]~~	+
-	~~[[Category: Pbcv-1]]~~	+
-	~~[[Category: Viral protein]]~~	+
-	~~[[Category: Vp54]]~~	+

OCA at 00:31, 10 February 2016

OCA — Wed, 10 Feb 2016 00:31:18 GMT

←Older revision		Revision as of 00:31, 10 February 2016
Line 15:		Line 15:
	<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=1j5q ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 03:34, 11 September 2015

OCA — Fri, 11 Sep 2015 03:34:59 GMT

←Older revision		Revision as of 03:34, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1j5q' size='340' side='right' caption='[[1j5q]], [[Resolution\|resolution]] 2.55Å' scene=''>		<StructureSection load='1j5q' size='340' side='right' caption='[[1j5q]], [[Resolution\|resolution]] 2.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1j5q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Paramecium_bursaria_chlorella_virus_1 Paramecium bursaria chlorella virus~~ 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J5Q FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1j5q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Chlorella_pbcv-1_virus Chlorella pbcv-1 virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J5Q FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m3y\|1m3y]], [[1m4x\|1m4x]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m3y\|1m3y]], [[1m4x\|1m4x]]</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=1j5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j5q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j5q RCSB], [http://www.ebi.ac.uk/pdbsum/1j5q 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=1j5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j5q OCA], [http://pdbe.org/1j5q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1j5q RCSB], [http://www.ebi.ac.uk/pdbsum/1j5q PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 1j5q" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Paramecium bursaria chlorella virus~~ 1]]	+	[[Category: Chlorella pbcv-1 virus]]
	[[Category: Baker, T S]]		[[Category: Baker, T S]]
	[[Category: Etten, J L.Van]]		[[Category: Etten, J L.Van]]

OCA at 12:19, 2 January 2015

OCA — Fri, 02 Jan 2015 12:19:25 GMT

←Older revision		Revision as of 12:19, 2 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1j5q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paramecium_bursaria_chlorella_virus_1 Paramecium bursaria chlorella virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J5Q FirstGlance]. <br>		<table><tr><td colspan='2'>[[1j5q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paramecium_bursaria_chlorella_virus_1 Paramecium bursaria chlorella virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J5Q FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m3y\|1m3y]], [[1m4x\|1m4x]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m3y\|1m3y]], [[1m4x\|1m4x]]</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=1j5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j5q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j5q RCSB], [http://www.ebi.ac.uk/pdbsum/1j5q 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=1j5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j5q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j5q RCSB], [http://www.ebi.ac.uk/pdbsum/1j5q 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: Paramecium bursaria chlorella virus 1]]		[[Category: Paramecium bursaria chlorella virus 1]]
-	[[Category: Baker, T S.]]	+	[[Category: Baker, T S]]
-	[[Category: Etten, J L.Van.]]	+	[[Category: Etten, J L.Van]]
-	[[Category: Graves, M V.]]	+	[[Category: Graves, M V]]
-	[[Category: Gurnon, J R.]]	+	[[Category: Gurnon, J R]]
-	[[Category: Nandhagopal, N.]]	+	[[Category: Nandhagopal, N]]
-	[[Category: Rossmann, M G.]]	+	[[Category: Rossmann, M G]]
-	[[Category: Simpson, A A.]]	+	[[Category: Simpson, A A]]
-	[[Category: Yan, X.]]	+	[[Category: Yan, X]]
	[[Category: Chlorella virus]]		[[Category: Chlorella virus]]
	[[Category: Major capsid protein of large dna virus]]		[[Category: Major capsid protein of large dna virus]]

OCA at 13:42, 28 September 2014

OCA — Sun, 28 Sep 2014 13:42:59 GMT

←Older revision		Revision as of 13:42, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1j5q.~~png~~\|~~left~~\|200px]]	+	==The Structure and Evolution of the Major Capsid Protein of a Large, Lipid-containing, DNA virus.==
		+	<StructureSection load='1j5q' size='340' side='right' caption='[[1j5q]], [[Resolution\|resolution]] 2.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1j5q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paramecium_bursaria_chlorella_virus_1 Paramecium bursaria chlorella virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1J5Q FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1m3y\|1m3y]], [[1m4x\|1m4x]]</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=1j5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j5q OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1j5q RCSB], [http://www.ebi.ac.uk/pdbsum/1j5q 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/j5/1j5q_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 ==
		+	Paramecium bursaria Chlorella virus type 1 (PBCV-1) is a very large, icosahedral virus containing an internal membrane enclosed within a glycoprotein coat consisting of pseudohexagonal arrays of trimeric capsomers. Each capsomer is composed of three molecules of the major capsid protein, Vp54, the 2.0-A resolution structure of which is reported here. Four N-linked and two O-linked glycosylation sites were identified. The N-linked sites are associated with nonstandard amino acid motifs as a result of glycosylation by virus-encoded enzymes. Each monomer of the trimeric structure consists of two eight-stranded, antiparallel beta-barrel, "jelly-roll" domains related by a pseudo-sixfold rotation. The fold of the monomer and the pseudo-sixfold symmetry of the capsomer resembles that of the major coat proteins in the double-stranded DNA bacteriophage PRD1 and the double-stranded DNA human adenoviruses, as well as the viral proteins VP2-VP3 of picornaviruses. The structural similarities among these diverse groups of viruses, whose hosts include bacteria, unicellular eukaryotes, plants, and mammals, make it probable that their capsid proteins have evolved from a common ancestor that had already acquired a pseudo-sixfold organization. The trimeric capsid protein structure was used to produce a quasi-atomic model of the 1,900-A diameter PBCV-1 outer shell, based on fitting of the Vp54 crystal structure into a three-dimensional cryoelectron microscopy image reconstruction of the virus.

-	~~{{STRUCTURE_1j5q\| PDB=1j5q \| SCENE= }}~~	+	The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus.,Nandhagopal N, Simpson AA, Gurnon JR, Yan X, Baker TS, Graves MV, Van Etten JL, Rossmann MG Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):14758-63. Epub 2002 Oct 31. PMID:12411581<ref>PMID:12411581</ref>

-	~~===The Structure and Evolution~~ of the ~~Major Capsid Protein~~ of ~~a Large, Lipid-containing, DNA virus~~.~~===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12411581}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1j5q]] is a 2 chain structure with sequence from [http:~~//en.wikipedia.org/wiki/Paramecium_bursaria_chlorella_virus_1 Paramecium bursaria chlorella virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5Q OCA].	+

	==See Also==		==See Also==
	*[[Virus coat protein\|Virus coat protein]]		*[[Virus coat protein\|Virus coat protein]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:012411581<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Paramecium bursaria chlorella virus 1]]		[[Category: Paramecium bursaria chlorella virus 1]]
	[[Category: Baker, T S.]]		[[Category: Baker, T S.]]

OCA: Protected "1j5q" [edit=sysop:move=sysop]

OCA — Sat, 20 Oct 2012 15:40:42 GMT

Protected "1j5q" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:40, 20 October 2012

OCA at 15:40, 20 October 2012

OCA — Sat, 20 Oct 2012 15:40:40 GMT

←Older revision		Revision as of 15:40, 20 October 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1j5q.png\|left\|200px]]		[[Image:1j5q.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1j5q", 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_1j5q\| PDB=1j5q \| SCENE= }}		{{STRUCTURE_1j5q\| PDB=1j5q \| SCENE= }}

	===The Structure and Evolution of the Major Capsid Protein of a Large, Lipid-containing, DNA virus.===		===The Structure and Evolution of the Major Capsid Protein of a Large, Lipid-containing, DNA virus.===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12411581}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12411581 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12411581}}		{{ABSTRACT_PUBMED_12411581}}

	==About this Structure==		==About this Structure==
-	~~1J5Q~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Paramecium_bursaria_chlorella_virus_1 Paramecium bursaria chlorella virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5Q OCA].	+	[[1j5q]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Paramecium_bursaria_chlorella_virus_1 Paramecium bursaria chlorella virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5Q OCA].
		+
		+	==See Also==
		+	*[[Virus coat protein\|Virus coat protein]]

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12411581~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012411581</ref><references group="xtra"/>
	[[Category: Paramecium bursaria chlorella virus 1]]		[[Category: Paramecium bursaria chlorella virus 1]]
	[[Category: Baker, T S.]]		[[Category: Baker, T S.]]
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	[[Category: Major capsid protein of large dna virus]]		[[Category: Major capsid protein of large dna virus]]
	[[Category: Pbcv-1]]		[[Category: Pbcv-1]]
		+	[[Category: Viral protein]]
	[[Category: Vp54]]		[[Category: Vp54]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:58:35 2009''

OCA at 11:58, 17 February 2009

OCA — Tue, 17 Feb 2009 11:58:36 GMT

←Older revision		Revision as of 11:58, 17 February 2009
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	==About this Structure==		==About this Structure==
-	1J5Q is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Paramecium_bursaria_chlorella_virus_1 Paramecium bursaria chlorella virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5Q OCA].	+	1J5Q is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Paramecium_bursaria_chlorella_virus_1 Paramecium bursaria chlorella virus 1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1J5Q OCA].

	==Reference==		==Reference==
-	The structure and evolution of the major capsid protein of a large, lipid-containing DNA virus., Nandhagopal N, Simpson AA, Gurnon JR, Yan X, Baker TS, Graves MV, Van Etten JL, Rossmann MG, Proc Natl Acad Sci U S A. 2002 Nov 12;99(23):14758-63. Epub 2002 Oct 31. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12411581 12411581]~~	+	<ref group="xtra">PMID:12411581</ref><references group="xtra"/>
	[[Category: Paramecium bursaria chlorella virus 1]]		[[Category: Paramecium bursaria chlorella virus 1]]
-	[[Category: Single protein]]
	[[Category: Baker, T S.]]		[[Category: Baker, T S.]]
	[[Category: Etten, J L.Van.]]		[[Category: Etten, J L.Van.]]
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	[[Category: Vp54]]		[[Category: Vp54]]

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OCA at 11:32, 1 July 2008

OCA — Tue, 01 Jul 2008 11:32:31 GMT

←Older revision		Revision as of 11:32, 1 July 2008
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-	[[Image:1j5q.~~jpg~~\|left\|200px]]	+	{{Seed}}
		+	[[Image:1j5q.png\|left\|200px]]

	<!--		<!--
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	{{STRUCTURE_1j5q\| PDB=1j5q \| SCENE= }}		{{STRUCTURE_1j5q\| PDB=1j5q \| SCENE= }}

-	~~'''~~The Structure and Evolution of the Major Capsid Protein of a Large, Lipid-containing, DNA virus.~~'''~~	+	===The Structure and Evolution of the Major Capsid Protein of a Large, Lipid-containing, DNA virus.===


-	~~==Overview==~~	+	<!--
-	~~Paramecium bursaria Chlorella virus type 1 (PBCV~~-1) is a very large, icosahedral virus containing an internal membrane enclosed within a glycoprotein coat consisting of pseudohexagonal arrays of trimeric capsomers. Each capsomer is composed of three molecules of the major capsid protein, Vp54, the 2.0-~~A resolution structure of which is reported here. Four N-linked and two O-linked glycosylation sites were identified.~~ The ~~N-linked sites are associated with nonstandard amino acid motifs as a result of glycosylation by virus-encoded enzymes. Each monomer of the trimeric structure consists of two eight-stranded~~, ~~antiparallel beta-barrel~~, ~~"jelly-roll" domains related by a pseudo-sixfold rotation. The fold of~~ the ~~monomer and~~ the ~~pseudo-sixfold symmetry of the capsomer resembles that of the major coat proteins in the double-stranded DNA bacteriophage PRD1 and the double-stranded DNA human adenoviruses,~~ as ~~well as the viral proteins VP2-VP3 of picornaviruses~~. ~~The structural similarities among these diverse groups of viruses~~, whose hosts include bacteria, unicellular eukaryotes, plants, and mammals, make it probable that their capsid proteins have evolved from a common ancestor that had already acquired a pseudo-sixfold organization. ~~The trimeric capsid protein structure was used to produce a quasi~~-~~atomic model of the 1,900~~-~~A diameter PBCV-1 outer shell, based on fitting of the Vp54 crystal structure into a three-dimensional cryoelectron microscopy image reconstruction of the virus.~~	+	The line below this paragraph, {{ABSTRACT_PUBMED_12411581}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 12411581 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_12411581}}

	==About this Structure==		==About this Structure==
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	[[Category: Pbcv-1]]		[[Category: Pbcv-1]]
	[[Category: Vp54]]		[[Category: Vp54]]
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OCA at 17:50, 2 May 2008

OCA — Fri, 02 May 2008 17:50:26 GMT

←Older revision		Revision as of 17:50, 2 May 2008
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	[[Image:1j5q.jpg\|left\|200px]]		[[Image:1j5q.jpg\|left\|200px]]

-	~~{{Structure~~	+	<!--
-	~~\|PDB= 1j5q \|SIZE=350\|CAPTION= <scene name='initialview01'>1j5q</scene>~~, ~~resolution 2~~.~~55Å~~	+	The line below this paragraph, containing "STRUCTURE_1j5q", creates the "Structure Box" on the page.
-	~~\|SITE=~~	+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	~~\|LIGAND= <~~scene ~~name='pdbligand=HG:MERCURY+(II~~)~~+ION'>HG</scene>~~, ~~<scene name='pdbligand=MAN:ALPHA~~-D-~~MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=NDG:2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE'>NDG</scene~~>	+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	\|~~ACTIVITY~~=	+	or leave the SCENE parameter empty for the default display.
-	\|~~GENE~~=	+	-->
-	~~\|DOMAIN=~~	+	{{STRUCTURE_1j5q\| PDB=1j5q \| SCENE= }}
-	~~\|RELATEDENTRY=[[1m3y\|1M3Y]], [[1m4x\|1M4X]]~~	+
-	\|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1j5q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1j5q OCA], [http://www.ebi.ac.uk/pdbsum/1j5q PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1j5q RCSB]</span>	+
-	}}	+

	'''The Structure and Evolution of the Major Capsid Protein of a Large, Lipid-containing, DNA virus.'''		'''The Structure and Evolution of the Major Capsid Protein of a Large, Lipid-containing, DNA virus.'''
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	[[Category: Simpson, A A.]]		[[Category: Simpson, A A.]]
	[[Category: Yan, X.]]		[[Category: Yan, X.]]
-	[[Category: ~~chlorella~~ virus]]	+	[[Category: Chlorella virus]]
-	[[Category: ~~major~~ capsid protein of large dna virus]]	+	[[Category: Major capsid protein of large dna virus]]
-	[[Category: ~~pbcv~~-1]]	+	[[Category: Pbcv-1]]
-	[[Category: ~~vp54~~]]	+	[[Category: Vp54]]
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