2df7 - Revision history

OCA at 08:26, 25 October 2023

2023-10-25T08:26:20Z

← Older revision		Revision as of 08:26, 25 October 2023
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	<StructureSection load='2df7' size='340' side='right'caption='[[2df7]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2df7' size='340' side='right'caption='[[2df7]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2df7]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Avian_infectious_bursal_disease_virus Avian infectious~~ bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DF7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2df7]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Infectious_bursal_disease_virus Infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DF7 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~</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]] 2.6Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height~~: ~~3em;~~'>~~[[1wcd\|1wcd]], [[1wce\|1wce]]~~</~~div~~></td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2df7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df7 OCA], [https://pdbe.org/2df7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2df7 RCSB], [https://www.ebi.ac.uk/pdbsum/2df7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2df7 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=2df7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df7 OCA], [https://pdbe.org/2df7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2df7 RCSB], [https://www.ebi.ac.uk/pdbsum/2df7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2df7 ProSAT]</span></td></tr>
	</table>		</table>
			== Function ==
			[https://www.uniprot.org/uniprot/Q9WR38_IBDV Q9WR38_IBDV] Capsid protein VP2 self assembles to form an icosahedral capsid with a T=13 symmetry, about 70 nm in diameter, and consisting of 260 VP2 trimers. The capsid encapsulates the genomic dsRNA. VP2 is also involved in attachment and entry into the host cell by interacting with host ITGA4/ITGB1.[ARBA:ARBA00024715] Capsid protein VP3 plays a key role in virion assembly by providing a scaffold for the capsid made of VP2. May self-assemble to form a T=4-like icosahedral inner-capsid composed of at least 180 trimers. Plays a role in genomic RNA packaging by recruiting VP1 into the capsid and interacting with the dsRNA genome segments to form a ribonucleoprotein complex. Additionally, the interaction of the VP3 C-terminal tail with VP1 removes the inherent structural blockade of the polymerase active site. Thus, VP3 can also function as a transcriptional activator.[ARBA:ARBA00025351][RuleBase:RU363030] Protease VP4 is a serine protease that cleaves the polyprotein into its final products. Pre-VP2 is first partially cleaved, and may be completely processed by VP4 upon capsid maturation.[PROSITE-ProRule:PRU00881][RuleBase:RU363030] Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry.[ARBA:ARBA00025236][RuleBase:RU363030] Structural peptide 2 is a small peptide derived from pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing.[RuleBase:RU363030] Structural peptide 3 is a small peptide derived from pre-VP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing.[RuleBase:RU363030] The precursor of VP2 plays an important role in capsid assembly. First, pre-VP2 and VP2 oligomers assemble to form a procapsid. Then, the pre-VP2 intermediates may be processed into VP2 proteins by proteolytic cleavage mediated by VP4 to obtain the mature virion. The final capsid is composed of pentamers and hexamers but VP2 has a natural tendency to assemble into all-pentameric structures. Therefore pre-VP2 may be required to allow formation of the hexameric structures.[ARBA:ARBA00024831][RuleBase:RU363030]
	== 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: ~~Avian infectious~~ bursal disease virus]]		[[Category: Infectious bursal disease virus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Ko~~, T P~~]]		[[Category: Ko TP]]
	[[Category: Lee~~, C C~~]]		[[Category: Lee CC]]
	[[Category: Wang~~, A H~~]]		[[Category: Wang AH]]
	[[Category: Wang~~, M Y]]~~		[[Category: Wang MY]]
	~~[[Category: Epitope]]~~
	~~[[Category: Icosahedral capsid]]~~
	~~[[Category: Immunogen]]~~
	~~[[Category: Surface loop]]~~
	~~[[Category: Virus like particle~~]]

OCA at 06:50, 10 November 2021

2021-11-10T06:50:01Z

← Older revision		Revision as of 06:50, 10 November 2021
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	<StructureSection load='2df7' size='340' side='right'caption='[[2df7]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2df7' size='340' side='right'caption='[[2df7]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2df7]] is a 20 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Avian_infectious_bursal_disease_virus Avian infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DF7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2df7]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Avian_infectious_bursal_disease_virus Avian infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DF7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wcd\|1wcd]], [[1wce\|1wce]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wcd\|1wcd]], [[1wce\|1wce]]</div></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2df7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df7 OCA], [~~http~~://pdbe.org/2df7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2df7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2df7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2df7 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=2df7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df7 OCA], [https://pdbe.org/2df7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2df7 RCSB], [https://www.ebi.ac.uk/pdbsum/2df7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2df7 ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</div>		</div>
	<div class="pdbe-citations 2df7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2df7" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:57, 4 March 2020

2020-03-04T07:57:22Z

← Older revision		Revision as of 07:57, 4 March 2020
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	==Crystal structure of infectious bursal disease virus VP2 subviral particle==		==Crystal structure of infectious bursal disease virus VP2 subviral particle==
	<StructureSection load='2df7' size='340' side='right' caption='[[2df7]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2df7' size='340' side='right'caption='[[2df7]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2df7]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Avian_infectious_bursal_disease_virus Avian infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DF7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2df7]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Avian_infectious_bursal_disease_virus Avian infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DF7 FirstGlance]. <br>
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Avian infectious bursal disease virus]]		[[Category: Avian infectious bursal disease virus]]
			[[Category: Large Structures]]
	[[Category: Ko, T P]]		[[Category: Ko, T P]]
	[[Category: Lee, C C]]		[[Category: Lee, C C]]

OCA at 06:51, 30 May 2018

2018-05-30T06:51:03Z

← Older revision		Revision as of 06:51, 30 May 2018
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	==Crystal structure of infectious bursal disease virus VP2 subviral particle==		==Crystal structure of infectious bursal disease virus VP2 subviral particle==
	<StructureSection load='2df7' size='340' side='right' caption='[[2df7]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2df7' size='340' side='right' caption='[[2df7]], [[Resolution\|resolution]] 2.60Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wcd\|1wcd]], [[1wce\|1wce]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wcd\|1wcd]], [[1wce\|1wce]]</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=2df7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df7 OCA], [http://pdbe.org/2df7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2df7 RCSB], [http://www.ebi.ac.uk/pdbsum/2df7 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=2df7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df7 OCA], [http://pdbe.org/2df7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2df7 RCSB], [http://www.ebi.ac.uk/pdbsum/2df7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2df7 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/df/2df7_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/df/2df7_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 03:22, 8 February 2016

2016-02-08T03:22:01Z

← Older revision		Revision as of 03:22, 8 February 2016
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2df7 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 07:23, 10 September 2015

2015-09-10T07:23:17Z

← Older revision		Revision as of 07:23, 10 September 2015
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	<StructureSection load='2df7' size='340' side='right' caption='[[2df7]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='2df7' size='340' side='right' caption='[[2df7]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2df7]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Infectious_bursal_disease_virus Infectious~~ bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DF7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2df7]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Avian_infectious_bursal_disease_virus Avian infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DF7 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wcd\|1wcd]], [[1wce\|1wce]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wcd\|1wcd]], [[1wce\|1wce]]</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=2df7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2df7 RCSB], [http://www.ebi.ac.uk/pdbsum/2df7 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=2df7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df7 OCA], [http://pdbe.org/2df7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2df7 RCSB], [http://www.ebi.ac.uk/pdbsum/2df7 PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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 2df7" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Infectious~~ bursal disease virus]]		[[Category: Avian infectious bursal disease virus]]
	[[Category: Ko, T P]]		[[Category: Ko, T P]]
	[[Category: Lee, C C]]		[[Category: Lee, C C]]

OCA at 17:11, 15 January 2015

2015-01-15T17:11:37Z

← Older revision		Revision as of 17:11, 15 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2df7]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Infectious_bursal_disease_virus Infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DF7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2df7]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Infectious_bursal_disease_virus Infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DF7 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wcd\|1wcd]], [[1wce\|1wce]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wcd\|1wcd]], [[1wce\|1wce]]</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=2df7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2df7 RCSB], [http://www.ebi.ac.uk/pdbsum/2df7 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=2df7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2df7 RCSB], [http://www.ebi.ac.uk/pdbsum/2df7 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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	</StructureSection>		</StructureSection>
	[[Category: Infectious bursal disease virus]]		[[Category: Infectious bursal disease virus]]
	[[Category: Ko, T P.]]		[[Category: Ko, T P]]
	[[Category: Lee, C C.]]		[[Category: Lee, C C]]
	[[Category: Wang, A H.]]		[[Category: Wang, A H]]
	[[Category: Wang, M Y.]]		[[Category: Wang, M Y]]
	[[Category: Epitope]]		[[Category: Epitope]]
	[[Category: Icosahedral capsid]]		[[Category: Icosahedral capsid]]

OCA at 00:32, 30 September 2014

2014-09-30T00:32:24Z

← Older revision		Revision as of 00:32, 30 September 2014
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	[[Image:~~2df7~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of infectious bursal disease virus VP2 subviral particle==
			<StructureSection load='2df7' size='340' side='right' caption='[[2df7]], [[Resolution\|resolution]] 2.60Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2df7]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/Infectious_bursal_disease_virus Infectious bursal disease virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DF7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DF7 FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wcd\|1wcd]], [[1wce\|1wce]]</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=2df7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2df7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2df7 RCSB], [http://www.ebi.ac.uk/pdbsum/2df7 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/df/2df7_consurf.spt"</scriptWhenChecked>
			<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
			<text>to colour the structure by Evolutionary Conservation</text>
			</jmolCheckbox>
			</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
			<div style="clear:both"></div>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			The structural protein VP2 of infectious bursal disease virus (IBDV) spontaneously forms a dodecahedral T=1 subviral particle (SVP), and is a primary immunogen of the virus. In this study, the structure of IBDV SVP was determined in a cubic crystal and refined to 2.6A resolution. It contains 20 independent VP2 subunits in a crystallographic asymmetric unit. Each subunit is folded mainly into a shell domain and a protrusion domain, both with the Swiss-roll topology, plus a small helical base domain. Three VP2 subunits constitute a tight trimer, which is the building block of IBDV (sub)viral particles. The structure revealed a calcium ion bound to three pairs of symmetry-related Asp31 and Asp174 to stabilize the VP2 trimer. Our results of treatment of SVP with EGTA, a Ca(2+)-chelating reagent, indicated that the metal-ion may be important not only in maintaining highly stable quaternary structure but also in regulating the swelling and dissociation of the icosahedral particles. A Ca(2+)-dependent assembly pathway was thus proposed, which involves further interactions between the trimers. The 20 independent subunits showed conformational variations, with the surface loops of the protrusion domain being the most diverse. These loops are targets of the neutralizing antibodies. Several common interactions between the surface loops were clearly observed, suggesting a possible major conformation of the immunogenic epitopes.

	~~{{STRUCTURE_2df7\| PDB=2df7 \| SCENE= }}~~		Crystal structure of infectious bursal disease virus VP2 subviral particle at 2.6A resolution: implications in virion assembly and immunogenicity.,Lee CC, Ko TP, Chou CC, Yoshimura M, Doong SR, Wang MY, Wang AH J Struct Biol. 2006 Jul;155(1):74-86. Epub 2006 Mar 31. PMID:16677827<ref>PMID:16677827</ref>

	~~===Crystal structure~~ of ~~infectious bursal disease virus VP2 subviral particle===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_16677827}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2df7]] is a 20 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Infectious_bursal_disease_virus Infectious bursal disease virus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DF7 OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:016677827<~~/~~ref><ref group="xtra">PMID:012832770</ref~~><~~references group="xtra"~~/>
	[[Category: Infectious bursal disease virus]]		[[Category: Infectious bursal disease virus]]
	[[Category: Ko, T P.]]		[[Category: Ko, T P.]]

OCA at 12:32, 23 January 2013

2013-01-23T12:32:31Z

← Older revision		Revision as of 12:32, 23 January 2013
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	[[Image:2df7.png\|left\|200px]]		[[Image:2df7.png\|left\|200px]]

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	{{STRUCTURE_2df7\| PDB=2df7 \| SCENE= }}		{{STRUCTURE_2df7\| PDB=2df7 \| SCENE= }}

	===Crystal structure of infectious bursal disease virus VP2 subviral particle===		===Crystal structure of infectious bursal disease virus VP2 subviral particle===


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	{{ABSTRACT_PUBMED_16677827}}		{{ABSTRACT_PUBMED_16677827}}

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	==Reference==		==Reference==
	<ref group="xtra">PMID:~~16677827~~</ref><ref group="xtra">PMID:~~12832770~~</ref><references group="xtra"/>		<ref group="xtra">PMID:016677827</ref><ref group="xtra">PMID:012832770</ref><references group="xtra"/>
	[[Category: Infectious bursal disease virus]]		[[Category: Infectious bursal disease virus]]
	[[Category: Ko, T P.]]		[[Category: Ko, T P.]]
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	[[Category: Wang, A H.]]		[[Category: Wang, A H.]]
	[[Category: Wang, M Y.]]		[[Category: Wang, M Y.]]
	~~[[Category: Calcium]]~~
	[[Category: Epitope]]		[[Category: Epitope]]
	[[Category: Icosahedral capsid]]		[[Category: Icosahedral capsid]]

OCA: Protected "2df7" [edit=sysop:move=sysop]

2011-03-14T19:19:35Z

Protected "2df7" [edit=sysop:move=sysop]

← Older revision	Revision as of 19:19, 14 March 2011
(No difference)