2z7j - Revision history

OCA at 09:24, 21 February 2024

OCA — Wed, 21 Feb 2024 09:24:59 GMT

←Older revision		Revision as of 09:24, 21 February 2024
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	<StructureSection load='2z7j' size='340' side='right'caption='[[2z7j]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='2z7j' size='340' side='right'caption='[[2z7j]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z7j]] is a 1 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=2Z7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z7j]] is a 1 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=2Z7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z7J FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=AU:GOLD+ION'>AU</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]] 2.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2r18\|2r18]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AU:GOLD+ION'>AU</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=2z7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7j OCA], [https://pdbe.org/2z7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z7j RCSB], [https://www.ebi.ac.uk/pdbsum/2z7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z7j 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=2z7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7j OCA], [https://pdbe.org/2z7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z7j RCSB], [https://www.ebi.ac.uk/pdbsum/2z7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z7j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/POLS_IBDVP POLS_IBDVP]] 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry (By similarity). Structural peptide 2 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 3 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 4 is a small peptide derived from pVP2 C-terminus. It is essential for the virus viability (By similarity).	+	[https://www.uniprot.org/uniprot/POLS_IBDVP POLS_IBDVP] 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry (By similarity). Structural peptide 2 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 3 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 4 is a small peptide derived from pVP2 C-terminus. It is essential for the virus viability (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=2z7j 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=2z7j ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Infectious bursal disease virus (IBDV), a member of the Birnaviridae family, is the causative agent of one of the most harmful poultry diseases. The IBDV genome encodes five mature proteins; of these, the multifunctional protein VP3 plays an essential role in virus morphogenesis. This protein, which interacts with the structural protein VP2, with the double-stranded RNA genome, and with the virus-encoded, RNA-dependent RNA polymerase, VP1, is involved not only in the formation of the viral capsid, but also in the recruitment of VP1 into the capsid and in the encapsidation of the viral genome. Here, we report the X-ray structure of the central region of VP3, residues 92-220, consisting of two alpha-helical domains connected by a long and flexible hinge that are organized as a dimer. Unexpectedly, the overall fold of the second VP3 domain shows significant structural similarities with different transcription regulation factors.
-
-	Structural insights into the multifunctional protein VP3 of birnaviruses.,Casanas A, Navarro A, Ferrer-Orta C, Gonzalez D, Rodriguez JF, Verdaguer N Structure. 2008 Jan;16(1):29-37. PMID:18184581<ref>PMID:18184581</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2z7j" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]		*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Avian infectious~~ bursal disease virus]]	+	[[Category: Infectious bursal disease virus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Casanas, A]]	+	[[Category: Casanas A]]
-	[[Category: Ferrer-Orta, C]]	+	[[Category: Ferrer-Orta C]]
-	[[Category: Gonzalez, D]]	+	[[Category: Gonzalez D]]
-	[[Category: Navarro, A]]	+	[[Category: Navarro A]]
-	[[Category: Rodriguez~~, J F~~]]	+	[[Category: Rodriguez JF]]
-	[[Category: Verdaguer, N]]	+	[[Category: Verdaguer N]]
-	~~[[Category: Capsid protein]]~~	+
-	~~[[Category: Helix]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Protease]]~~	+
-	~~[[Category: Serine protease]]~~	+
-	~~[[Category: Viral protein]]~~	+
-	~~[[Category: Virion~~]]	+

OCA at 10:47, 8 December 2021

OCA — Wed, 08 Dec 2021 10:47:36 GMT

←Older revision		Revision as of 10:47, 8 December 2021
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	<StructureSection load='2z7j' size='340' side='right'caption='[[2z7j]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='2z7j' size='340' side='right'caption='[[2z7j]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z7j]] is a 1 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=2Z7J OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2Z7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z7j]] is a 1 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=2Z7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Z7J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r18\|2r18]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2r18\|2r18]]</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=2z7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7j OCA], [~~http~~://pdbe.org/2z7j PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2z7j RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2z7j PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2z7j 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=2z7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7j OCA], [https://pdbe.org/2z7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2z7j RCSB], [https://www.ebi.ac.uk/pdbsum/2z7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2z7j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/POLS_IBDVP POLS_IBDVP]] 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry (By similarity). Structural peptide 2 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 3 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 4 is a small peptide derived from pVP2 C-terminus. It is essential for the virus viability (By similarity).	+	[[https://www.uniprot.org/uniprot/POLS_IBDVP POLS_IBDVP]] 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry (By similarity). Structural peptide 2 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 3 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 4 is a small peptide derived from pVP2 C-terminus. It is essential for the virus viability (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	==See Also==		==See Also==
-	*[[Virus coat ~~protein~~\|Virus coat ~~protein~~]]	+	*[[Virus coat proteins 3D structures\|Virus coat proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:30, 31 July 2019

OCA — Wed, 31 Jul 2019 07:30:22 GMT

←Older revision		Revision as of 07:30, 31 July 2019
Line 1:		Line 1:

	==Structural insights into de multifunctional VP3 protein of birnaviruses:gold derivative==		==Structural insights into de multifunctional VP3 protein of birnaviruses:gold derivative==
-	<StructureSection load='2z7j' size='340' side='right' caption='[[2z7j]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='2z7j' size='340' side='right'caption='[[2z7j]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2z7j]] is a 1 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=2Z7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z7J FirstGlance]. <br>		<table><tr><td colspan='2'>[[2z7j]] is a 1 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=2Z7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z7J FirstGlance]. <br>
Line 14:		Line 14:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z7/2z7j_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/z7/2z7j_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 29:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2z7j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2z7j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Virus coat protein\|Virus coat protein]]
	== References ==		== References ==
	<references/>		<references/>
Line 34:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Avian infectious bursal disease virus]]		[[Category: Avian infectious bursal disease virus]]
		+	[[Category: Large Structures]]
	[[Category: Casanas, A]]		[[Category: Casanas, A]]
	[[Category: Ferrer-Orta, C]]		[[Category: Ferrer-Orta, C]]

OCA at 15:25, 12 October 2017

OCA — Thu, 12 Oct 2017 15:25:57 GMT

←Older revision		Revision as of 15:25, 12 October 2017
Line 1:		Line 1:
		+
	==Structural insights into de multifunctional VP3 protein of birnaviruses:gold derivative==		==Structural insights into de multifunctional VP3 protein of birnaviruses:gold derivative==
	<StructureSection load='2z7j' size='340' side='right' caption='[[2z7j]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='2z7j' size='340' side='right' caption='[[2z7j]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r18\|2r18]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r18\|2r18]]</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=2z7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7j OCA], [http://pdbe.org/2z7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z7j RCSB], [http://www.ebi.ac.uk/pdbsum/2z7j 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=2z7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7j OCA], [http://pdbe.org/2z7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z7j RCSB], [http://www.ebi.ac.uk/pdbsum/2z7j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2z7j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 29:
	</div>		</div>
	<div class="pdbe-citations 2z7j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 2z7j" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Virus coat protein\|Virus coat protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 08:45, 7 February 2016

OCA — Sun, 07 Feb 2016 08:45:43 GMT

←Older revision		Revision as of 08:45, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='2z7j' size='340' side='right' caption='[[2z7j]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='2z7j' size='340' side='right' caption='[[2z7j]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2z7j]] is a 1 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=2Z7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z7J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2z7j]] is a 1 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=2Z7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z7J FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r18\|2r18]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r18\|2r18]]</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=2z7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z7j RCSB], [http://www.ebi.ac.uk/pdbsum/2z7j 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=2z7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7j OCA], [http://pdbe.org/2z7j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2z7j RCSB], [http://www.ebi.ac.uk/pdbsum/2z7j PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 17:
	<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=2z7j ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 27:
	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 2z7j" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 35:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Infectious~~ bursal disease virus]]	+	[[Category: Avian infectious bursal disease virus]]
	[[Category: Casanas, A]]		[[Category: Casanas, A]]
	[[Category: Ferrer-Orta, C]]		[[Category: Ferrer-Orta, C]]

OCA at 13:44, 24 December 2014

OCA — Wed, 24 Dec 2014 13:44:47 GMT

←Older revision		Revision as of 13:44, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2z7j]] is a 1 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=2Z7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z7J FirstGlance]. <br>		<table><tr><td colspan='2'>[[2z7j]] is a 1 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=2Z7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z7J FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r18\|2r18]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r18\|2r18]]</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=2z7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z7j RCSB], [http://www.ebi.ac.uk/pdbsum/2z7j 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=2z7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z7j RCSB], [http://www.ebi.ac.uk/pdbsum/2z7j PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/POLS_IBDVP POLS_IBDVP]] 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 (By similarity). 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 (By similarity). 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 (By similarity). 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 (By similarity). Structural peptide 1 is a small peptide derived from pre-VP2 C-terminus. It destabilizes and perforates cell membranes, suggesting a role during entry (By similarity). Structural peptide 2 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 3 is a small peptide derived from pVP2 C-terminus. It is not essential for the virus viability, but viral growth is affected when missing (By similarity). Structural peptide 4 is a small peptide derived from pVP2 C-terminus. It is essential for the virus viability (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 25:		Line 27:
	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>
		+
		+	==See Also==
		+	*[[Virus coat protein\|Virus coat protein]]
	== References ==		== References ==
	<references/>		<references/>
Line 30:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Infectious bursal disease virus]]		[[Category: Infectious bursal disease virus]]
-	[[Category: Casanas, A.]]	+	[[Category: Casanas, A]]
-	[[Category: Ferrer-Orta, C.]]	+	[[Category: Ferrer-Orta, C]]
-	[[Category: Gonzalez, D.]]	+	[[Category: Gonzalez, D]]
-	[[Category: Navarro, A.]]	+	[[Category: Navarro, A]]
-	[[Category: Rodriguez, J F.]]	+	[[Category: Rodriguez, J F]]
-	[[Category: Verdaguer, N.]]	+	[[Category: Verdaguer, N]]
	[[Category: Capsid protein]]		[[Category: Capsid protein]]
	[[Category: Helix]]		[[Category: Helix]]

OCA at 05:24, 2 October 2014

OCA — Thu, 02 Oct 2014 05:24:21 GMT

←Older revision		Revision as of 05:24, 2 October 2014
Line 1:		Line 1:
-	[[~~Image:~~2z7j.~~png~~\|~~left~~\|200px]]	+	==Structural insights into de multifunctional VP3 protein of birnaviruses:gold derivative==
		+	<StructureSection load='2z7j' size='340' side='right' caption='[[2z7j]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2z7j]] is a 1 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=2Z7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Z7J FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AU:GOLD+ION'>AU</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2r18\|2r18]]</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=2z7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2z7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2z7j RCSB], [http://www.ebi.ac.uk/pdbsum/2z7j 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/z7/2z7j_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 ==
		+	Infectious bursal disease virus (IBDV), a member of the Birnaviridae family, is the causative agent of one of the most harmful poultry diseases. The IBDV genome encodes five mature proteins; of these, the multifunctional protein VP3 plays an essential role in virus morphogenesis. This protein, which interacts with the structural protein VP2, with the double-stranded RNA genome, and with the virus-encoded, RNA-dependent RNA polymerase, VP1, is involved not only in the formation of the viral capsid, but also in the recruitment of VP1 into the capsid and in the encapsidation of the viral genome. Here, we report the X-ray structure of the central region of VP3, residues 92-220, consisting of two alpha-helical domains connected by a long and flexible hinge that are organized as a dimer. Unexpectedly, the overall fold of the second VP3 domain shows significant structural similarities with different transcription regulation factors.

-	~~{{STRUCTURE_2z7j\| PDB=2z7j \| SCENE= }}~~	+	Structural insights into the multifunctional protein VP3 of birnaviruses.,Casanas A, Navarro A, Ferrer-Orta C, Gonzalez D, Rodriguez JF, Verdaguer N Structure. 2008 Jan;16(1):29-37. PMID:18184581<ref>PMID:18184581</ref>

-	~~===Structural insights into de multifunctional VP3 protein~~ of ~~birnaviruses:gold derivative===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_18184581}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2z7j]] is a 1 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=2Z7J OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:018184581<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Infectious bursal disease virus]]		[[Category: Infectious bursal disease virus]]
	[[Category: Casanas, A.]]		[[Category: Casanas, A.]]

OCA: Protected "2z7j" [edit=sysop:move=sysop]

OCA — Mon, 07 Jan 2013 20:05:33 GMT

Protected "2z7j" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:05, 7 January 2013

OCA at 20:05, 7 January 2013

OCA — Mon, 07 Jan 2013 20:05:31 GMT

←Older revision		Revision as of 20:05, 7 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:2z7j.png\|left\|200px]]		[[Image:2z7j.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_2z7j", 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_2z7j\| PDB=2z7j \| SCENE= }}		{{STRUCTURE_2z7j\| PDB=2z7j \| SCENE= }}

	===Structural insights into de multifunctional VP3 protein of birnaviruses:gold derivative===		===Structural insights into de multifunctional VP3 protein of birnaviruses:gold derivative===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_18184581}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 18184581 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_18184581}}		{{ABSTRACT_PUBMED_18184581}}

	==About this Structure==		==About this Structure==
-	~~2Z7J~~ is a 1 chain structure of 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=2Z7J OCA].	+	[[2z7j]] is a 1 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=2Z7J OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~18184581~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:018184581</ref><references group="xtra"/>
	[[Category: Infectious bursal disease virus]]		[[Category: Infectious bursal disease virus]]
	[[Category: Casanas, A.]]		[[Category: Casanas, A.]]
Line 38:		Line 26:
	[[Category: Viral protein]]		[[Category: Viral protein]]
	[[Category: Virion]]		[[Category: Virion]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:40:27 2009''

OCA at 10:40, 16 February 2009

OCA — Mon, 16 Feb 2009 10:40:28 GMT

←Older revision		Revision as of 10:40, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2Z7J is a ~~[[Single protein]]~~ structure of 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=2Z7J OCA].	+	2Z7J is a 1 chain structure of 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=2Z7J OCA].

	==Reference==		==Reference==
-	~~Structural insights into the multifunctional protein VP3 of birnaviruses., Casanas A, Navarro A, Ferrer-Orta C, Gonzalez D, Rodriguez JF, Verdaguer N, Structure. 2008 Jan;16(1):29-37.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/18184581 18184581]~~	+	<ref group="xtra">PMID:18184581</ref><references group="xtra"/>
	[[Category: Infectious bursal disease virus]]		[[Category: Infectious bursal disease virus]]
-	[[Category: Single protein]]
	[[Category: Casanas, A.]]		[[Category: Casanas, A.]]
	[[Category: Ferrer-Orta, C.]]		[[Category: Ferrer-Orta, C.]]
Line 40:		Line 39:
	[[Category: Virion]]		[[Category: Virion]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 14~~:56:~~29 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 12:40:27 2009''