3evd - Revision history

OCA at 06:35, 6 September 2023

2023-09-06T06:35:59Z

← Older revision		Revision as of 06:35, 6 September 2023
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	<StructureSection load='3evd' size='340' side='right'caption='[[3evd]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='3evd' size='340' side='right'caption='[[3evd]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3evd]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Yefv1 Yefv1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EVD OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=3EVD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3evd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Yellow_fever_virus_17D Yellow fever virus 17D]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EVD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EVD FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=GTP:GUANOSINE~~-5~~-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</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]] 1.5Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[3eva\|3eva]]~~, ~~[[3evb\|3evb]], [[3evc\|3evc]], [[3eve\|3eve]], [[3evf\|3evf]], [[3evg\|3evg]]~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=3evd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3evd OCA], [~~http~~://pdbe.org/3evd PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3evd RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3evd PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3evd 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=3evd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3evd OCA], [https://pdbe.org/3evd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3evd RCSB], [https://www.ebi.ac.uk/pdbsum/3evd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3evd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/POLG_YEFV1 POLG_YEFV1]] Capsid protein C self-assembles to form an icosahedral capsid about 30 nm in diameter. The capsid encapsulates the genomic RNA (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> prM acts as a chaperone for envelope protein E during intracellular virion assembly by masking and inactivating envelope protein E fusion peptide. prM is matured in the last step of virion assembly, presumably to avoid catastrophic activation of the viral fusion peptide induced by the acidic pH of the trans-Golgi network. After cleavage by host furin, the pr peptide is released in the extracellular medium and small envelope protein M and envelope protein E homodimers are dissociated (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Envelope protein E binding to host cell surface receptor is followed by virus internalization through clathrin-mediated endocytosis. Envelope protein E is subsequently involved in membrane fusion between virion and host late endosomes. Synthesized as a homodimer with prM which acts as a chaperone for envelope protein E. After cleavage of prM, envelope protein E dissociate from small envelope protein M and homodimerizes (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Non-structural protein 1 is involved in virus replication and regulation of the innate immune response (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Non-structural protein 2A may be involved viral RNA replication and capsid assembly (Potential).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Non-structural protein 2B is a required cofactor for the serine protease function of NS3 (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Serine protease NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS3 serine protease, in association with NS2B, performs its autocleavage and cleaves the polyprotein at dibasic sites in the cytoplasm: C-prM, NS2A-NS2B, NS2B-NS3, NS3-NS4A, NS4A-2K and NS4B-NS5. NS3 RNA helicase binds RNA and unwinds dsRNA in the 3' to 5' direction (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Non-structural protein 4A induces host endoplasmic reticulum membrane rearrangements leading to the formation of virus-induced membranous vesicles hosting the dsRNA and polymerase, functioning as a replication complex. NS4A might also regulate the ATPase activity of the NS3 helicase (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Peptide 2k functions as a signal peptide for NS4B and is required for the interferon antagonism activity of the latter (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Non-structural protein 4B inhibits interferon (IFN)-induced host STAT1 phosphorylation and nuclear translocation, thereby preventing the establishment of cellular antiviral state by blocking the IFN-alpha/beta pathway (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome, and performs the capping of genomes in the cytoplasm. NS5 methylates viral RNA cap at guanine N-7 and ribose 2'-O positions. Besides its role in genome replication, also prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) signaling pathway (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref>		[https://www.uniprot.org/uniprot/POLG_YEFV1 POLG_YEFV1] Capsid protein C self-assembles to form an icosahedral capsid about 30 nm in diameter. The capsid encapsulates the genomic RNA (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> prM acts as a chaperone for envelope protein E during intracellular virion assembly by masking and inactivating envelope protein E fusion peptide. prM is matured in the last step of virion assembly, presumably to avoid catastrophic activation of the viral fusion peptide induced by the acidic pH of the trans-Golgi network. After cleavage by host furin, the pr peptide is released in the extracellular medium and small envelope protein M and envelope protein E homodimers are dissociated (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Envelope protein E binding to host cell surface receptor is followed by virus internalization through clathrin-mediated endocytosis. Envelope protein E is subsequently involved in membrane fusion between virion and host late endosomes. Synthesized as a homodimer with prM which acts as a chaperone for envelope protein E. After cleavage of prM, envelope protein E dissociate from small envelope protein M and homodimerizes (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Non-structural protein 1 is involved in virus replication and regulation of the innate immune response (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Non-structural protein 2A may be involved viral RNA replication and capsid assembly (Potential).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Non-structural protein 2B is a required cofactor for the serine protease function of NS3 (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Serine protease NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS3 serine protease, in association with NS2B, performs its autocleavage and cleaves the polyprotein at dibasic sites in the cytoplasm: C-prM, NS2A-NS2B, NS2B-NS3, NS3-NS4A, NS4A-2K and NS4B-NS5. NS3 RNA helicase binds RNA and unwinds dsRNA in the 3' to 5' direction (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Non-structural protein 4A induces host endoplasmic reticulum membrane rearrangements leading to the formation of virus-induced membranous vesicles hosting the dsRNA and polymerase, functioning as a replication complex. NS4A might also regulate the ATPase activity of the NS3 helicase (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Peptide 2k functions as a signal peptide for NS4B and is required for the interferon antagonism activity of the latter (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Non-structural protein 4B inhibits interferon (IFN)-induced host STAT1 phosphorylation and nuclear translocation, thereby preventing the establishment of cellular antiviral state by blocking the IFN-alpha/beta pathway (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome, and performs the capping of genomes in the cytoplasm. NS5 methylates viral RNA cap at guanine N-7 and ribose 2'-O positions. Besides its role in genome replication, also prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) signaling pathway (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref>
	== 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: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Yefv1~~]]		[[Category: Yellow fever virus 17D]]
	[[Category: Geiss~~, B J~~]]		[[Category: Geiss BJ]]
	[[Category: Peersen~~, O B~~]]		[[Category: Peersen OB]]
	[[Category: Thompson~~, A A]]~~		[[Category: Thompson AA]]
	~~[[Category: Atp-binding]]~~
	~~[[Category: Capsid protein]]~~
	~~[[Category: Cleavage on pair of basic residue]]~~
	~~[[Category: Endoplasmic reticulum]]~~
	~~[[Category: Envelope protein]]~~
	~~[[Category: Glycoprotein]]~~
	~~[[Category: Helicase]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Membrane]]~~
	~~[[Category: Metal-binding]]~~
	~~[[Category: Multifunctional enzyme]]~~
	~~[[Category: Ns5 methyltransferase]]~~
	~~[[Category: Nucleotide-binding]]~~
	~~[[Category: Nucleotidyltransferase]]~~
	~~[[Category: Nucleus]]~~
	~~[[Category: Phosphoprotein]]~~
	~~[[Category: Protease]]~~
	~~[[Category: Ribonucleoprotein]]~~
	~~[[Category: Rna cap binding]]~~
	~~[[Category: Rna replication]]~~
	~~[[Category: Rna-binding]]~~
	~~[[Category: Rna-directed rna polymerase]]~~
	~~[[Category: Secreted]]~~
	~~[[Category: Serine protease]]~~
	~~[[Category: Transferase]]~~
	~~[[Category: Transmembrane]]~~
	~~[[Category: Viral nucleoprotein]]~~
	~~[[Category: Virion]]~~
	~~[[Category: Yellow fever virus~~]]

OCA at 10:25, 9 September 2020

2020-09-09T10:25:35Z

← Older revision		Revision as of 10:25, 9 September 2020
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	==Crystal structure of GTP complex of yellow fever virus methyltransferase and S-adenosyl-L-homocysteine==		==Crystal structure of GTP complex of yellow fever virus methyltransferase and S-adenosyl-L-homocysteine==
	<StructureSection load='3evd' size='340' side='right' caption='[[3evd]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='3evd' size='340' side='right'caption='[[3evd]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3evd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yefv1 Yefv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EVD OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3EVD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3evd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yefv1 Yefv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EVD OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3EVD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eva\|3eva]], [[3evb\|3evb]], [[3evc\|3evc]], [[3eve\|3eve]], [[3evf\|3evf]], [[3evg\|3evg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eva\|3eva]], [[3evb\|3evb]], [[3evc\|3evc]], [[3eve\|3eve]], [[3evf\|3evf]], [[3evg\|3evg]]</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=3evd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3evd OCA], [http://pdbe.org/3evd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3evd RCSB], [http://www.ebi.ac.uk/pdbsum/3evd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3evd ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3evd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3evd OCA], [http://pdbe.org/3evd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3evd RCSB], [http://www.ebi.ac.uk/pdbsum/3evd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3evd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 31:		Line 31:

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Large Structures]]
	[[Category: Yefv1]]		[[Category: Yefv1]]
	[[Category: Geiss, B J]]		[[Category: Geiss, B J]]

OCA at 22:04, 2 December 2018

2018-12-02T22:04:33Z

← Older revision		Revision as of 22:04, 2 December 2018
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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/ev/3evd_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ev/3evd_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 03:33, 5 August 2016

2016-08-05T03:33:45Z

← Older revision		Revision as of 03:33, 5 August 2016
Line 1:		Line 1:

	==Crystal structure of GTP complex of yellow fever virus methyltransferase and S-adenosyl-L-homocysteine==		==Crystal structure of GTP complex of yellow fever virus methyltransferase and S-adenosyl-L-homocysteine==
	<StructureSection load='3evd' size='340' side='right' caption='[[3evd]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='3evd' size='340' side='right' caption='[[3evd]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3evd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Yellow_fever_virus Yellow fever virus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EVD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EVD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3evd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yefv1 Yefv1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EVD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EVD FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eva\|3eva]], [[3evb\|3evb]], [[3evc\|3evc]], [[3eve\|3eve]], [[3evf\|3evf]], [[3evg\|3evg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eva\|3eva]], [[3evb\|3evb]], [[3evc\|3evc]], [[3eve\|3eve]], [[3evf\|3evf]], [[3evg\|3evg]]</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=3evd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3evd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3evd RCSB], [http://www.ebi.ac.uk/pdbsum/3evd 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=3evd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3evd OCA], [http://pdbe.org/3evd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3evd RCSB], [http://www.ebi.ac.uk/pdbsum/3evd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3evd ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	<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=3evd ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 27:		Line 28:
	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 3evd" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 34:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Yellow fever virus~~]]		[[Category: Yefv1]]
	[[Category: Geiss, B J]]		[[Category: Geiss, B J]]
	[[Category: Peersen, O B]]		[[Category: Peersen, O B]]
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	[[Category: Viral nucleoprotein]]		[[Category: Viral nucleoprotein]]
	[[Category: Virion]]		[[Category: Virion]]
			[[Category: Yellow fever virus]]

OCA at 15:31, 25 December 2014

2014-12-25T15:31:40Z

← Older revision		Revision as of 15:31, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3evd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yellow_fever_virus Yellow fever virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EVD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EVD FirstGlance]. <br>		<table><tr><td colspan='2'>[[3evd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yellow_fever_virus Yellow fever virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EVD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EVD FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eva\|3eva]], [[3evb\|3evb]], [[3evc\|3evc]], [[3eve\|3eve]], [[3evf\|3evf]], [[3evg\|3evg]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eva\|3eva]], [[3evb\|3evb]], [[3evc\|3evc]], [[3eve\|3eve]], [[3evf\|3evf]], [[3evg\|3evg]]</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=3evd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3evd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3evd RCSB], [http://www.ebi.ac.uk/pdbsum/3evd 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=3evd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3evd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3evd RCSB], [http://www.ebi.ac.uk/pdbsum/3evd PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/POLG_YEFV1 POLG_YEFV1]] Capsid protein C self-assembles to form an icosahedral capsid about 30 nm in diameter. The capsid encapsulates the genomic RNA (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> prM acts as a chaperone for envelope protein E during intracellular virion assembly by masking and inactivating envelope protein E fusion peptide. prM is matured in the last step of virion assembly, presumably to avoid catastrophic activation of the viral fusion peptide induced by the acidic pH of the trans-Golgi network. After cleavage by host furin, the pr peptide is released in the extracellular medium and small envelope protein M and envelope protein E homodimers are dissociated (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Envelope protein E binding to host cell surface receptor is followed by virus internalization through clathrin-mediated endocytosis. Envelope protein E is subsequently involved in membrane fusion between virion and host late endosomes. Synthesized as a homodimer with prM which acts as a chaperone for envelope protein E. After cleavage of prM, envelope protein E dissociate from small envelope protein M and homodimerizes (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Non-structural protein 1 is involved in virus replication and regulation of the innate immune response (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Non-structural protein 2A may be involved viral RNA replication and capsid assembly (Potential).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Non-structural protein 2B is a required cofactor for the serine protease function of NS3 (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Serine protease NS3 displays three enzymatic activities: serine protease, NTPase and RNA helicase. NS3 serine protease, in association with NS2B, performs its autocleavage and cleaves the polyprotein at dibasic sites in the cytoplasm: C-prM, NS2A-NS2B, NS2B-NS3, NS3-NS4A, NS4A-2K and NS4B-NS5. NS3 RNA helicase binds RNA and unwinds dsRNA in the 3' to 5' direction (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Non-structural protein 4A induces host endoplasmic reticulum membrane rearrangements leading to the formation of virus-induced membranous vesicles hosting the dsRNA and polymerase, functioning as a replication complex. NS4A might also regulate the ATPase activity of the NS3 helicase (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Peptide 2k functions as a signal peptide for NS4B and is required for the interferon antagonism activity of the latter (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> Non-structural protein 4B inhibits interferon (IFN)-induced host STAT1 phosphorylation and nuclear translocation, thereby preventing the establishment of cellular antiviral state by blocking the IFN-alpha/beta pathway (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref> RNA-directed RNA polymerase NS5 replicates the viral (+) and (-) genome, and performs the capping of genomes in the cytoplasm. NS5 methylates viral RNA cap at guanine N-7 and ribose 2'-O positions. Besides its role in genome replication, also prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) signaling pathway (By similarity).<ref>PMID:8189517</ref> <ref>PMID:9371625</ref> <ref>PMID:15956546</ref> <ref>PMID:17267492</ref> <ref>PMID:19850911</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Yellow fever virus]]		[[Category: Yellow fever virus]]
	[[Category: Geiss, B J.]]		[[Category: Geiss, B J]]
	[[Category: Peersen, O B.]]		[[Category: Peersen, O B]]
	[[Category: Thompson, A A.]]		[[Category: Thompson, A A]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Capsid protein]]		[[Category: Capsid protein]]
Line 64:		Line 66:
	[[Category: Viral nucleoprotein]]		[[Category: Viral nucleoprotein]]
	[[Category: Virion]]		[[Category: Virion]]
	~~[[Category: Yellow fever virus]]~~

OCA at 11:17, 29 September 2014

2014-09-29T11:17:21Z

← Older revision		Revision as of 11:17, 29 September 2014
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	[[Image:~~3evd~~.~~png~~\|~~left~~\|~~200px~~]]		==Crystal structure of GTP complex of yellow fever virus methyltransferase and S-adenosyl-L-homocysteine==
			<StructureSection load='3evd' size='340' side='right' caption='[[3evd]], [[Resolution\|resolution]] 1.50Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[3evd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yellow_fever_virus Yellow fever virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EVD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3EVD FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3eva\|3eva]], [[3evb\|3evb]], [[3evc\|3evc]], [[3eve\|3eve]], [[3evf\|3evf]], [[3evg\|3evg]]</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=3evd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3evd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3evd RCSB], [http://www.ebi.ac.uk/pdbsum/3evd 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/ev/3evd_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 flavivirus 2'-O-nucleoside N-terminal RNA methyltransferase (MTase) enzyme is responsible for methylating the viral RNA cap structure. To increase our understanding of the mechanism of viral RNA cap binding we performed a detailed structural and biochemical characterization of the guanosine cap-binding pocket of the dengue (DEN) and yellow fever (YF) virus MTase enzymes. We solved an improved 2.1 A resolution crystal structure of DEN2 Mtase, new 1.5 A resolution crystal structures of the YF virus MTase domain in apo form, and a new 1.45 A structure in complex with guanosine triphosphate and RNA cap analog. Our structures clarify the previously reported DEN MTase structure, suggest novel protein-cap interactions, and provide a detailed view of guanine specificity. Furthermore, the structures of the DEN and YF proteins are essentially identical, indicating a large degree of structural conservation amongst the flavivirus MTases. Guanosine triphosphate analog competition assays and mutagenesis analysis, performed to analyze the biochemical characteristics of cap binding, determined that the major interaction points are (i) guanine ring via pi-pi stacking with Phe24, N1 hydrogen interaction with the Leu19 backbone carbonyl via a water bridge, and C2 amine interaction with Leu16 and Leu19 backbone carbonyls; (ii) ribose 2' hydroxyl interaction with Lys13 and Asn17; and (iii) alpha-phosphate interactions with Lys28 and Ser215. Based on our mutational and analog studies, the guanine ring and alpha-phosphate interactions provide most of the energy for cap binding, while the combination of the water bridge between the guanine N1 and Leu19 carbonyl and the hydrogen bonds between the C2 amine and Leu16/Leu19 carbonyl groups provide for specific guanine recognition. A detailed model of how the flavivirus MTase protein binds RNA cap structures is presented.

	~~{{STRUCTURE_3evd\| PDB=3evd \| SCENE= }}~~		Analysis of Flavivirus NS5 Methyltransferase Cap Binding.,Geiss BJ, Thompson AA, Andrews AJ, Sons RL, Gari HH, Keenan SM, Peersen OB J Mol Biol. 2008 Dec 11. PMID:19101564<ref>PMID:19101564</ref>

	~~===Crystal structure~~ of ~~GTP complex of yellow fever virus methyltransferase and~~ S~~-adenosyl-L-homocysteine===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_19101564}}~~

	~~==About this Structure==~~
	~~[[3evd]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Yellow_fever_virus Yellow fever virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il~~/~~oca-bin/ocashort?id=3EVD OCA].~~

	==See Also==		==See Also==
	*[[RNA polymerase\|RNA polymerase]]		*[[RNA polymerase\|RNA polymerase]]
			== References ==
	==~~Reference~~==		<references/>
	<~~ref group="xtra">PMID:019101564<~~/~~ref~~><~~references group="xtra"~~/>		__TOC__
			</StructureSection>
	[[Category: Yellow fever virus]]		[[Category: Yellow fever virus]]
	[[Category: Geiss, B J.]]		[[Category: Geiss, B J.]]

OCA at 18:22, 20 October 2012

2012-10-20T18:22:07Z

← Older revision		Revision as of 18:22, 20 October 2012
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	==About this Structure==		==About this Structure==
	[[3evd]] is a 1 chain structure ~~of [[RNA polymerase]]~~ with sequence from [http://en.wikipedia.org/wiki/Yellow_fever_virus Yellow fever virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EVD OCA].		[[3evd]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yellow_fever_virus Yellow fever virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EVD OCA].

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

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

2012-07-27T03:52:03Z

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

← Older revision	Revision as of 03:52, 27 July 2012
(No difference)

OCA at 03:52, 27 July 2012

2012-07-27T03:52:01Z

← Older revision		Revision as of 03:52, 27 July 2012
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	~~{{Seed}}~~
	[[Image:3evd.png\|left\|200px]]		[[Image:3evd.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_3evd", 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_3evd\| PDB=3evd \| SCENE= }}		{{STRUCTURE_3evd\| PDB=3evd \| SCENE= }}

	===Crystal structure of GTP complex of yellow fever virus methyltransferase and S-adenosyl-L-homocysteine===		===Crystal structure of GTP complex of yellow fever virus methyltransferase and S-adenosyl-L-homocysteine===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_19101564}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 19101564 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_19101564}}		{{ABSTRACT_PUBMED_19101564}}

	==About this Structure==		==About this Structure==
	~~3EVD~~ is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Yellow_fever_virus_17d~~ Yellow fever virus ~~17d~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EVD OCA].		[[3evd]] is a 1 chain structure of [[RNA polymerase]] with sequence from [http://en.wikipedia.org/wiki/Yellow_fever_virus Yellow fever virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EVD OCA].

			==See Also==
			*[[RNA polymerase\|RNA polymerase]]

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~19101564~~</ref><references group="xtra"/>		<ref group="xtra">PMID:019101564</ref><references group="xtra"/>
	[[Category: Yellow fever virus ~~17d~~]]		[[Category: Yellow fever virus]]
	[[Category: Geiss, B J.]]		[[Category: Geiss, B J.]]
	[[Category: Peersen, O B.]]		[[Category: Peersen, O B.]]
Line 52:		Line 43:
	[[Category: Secreted]]		[[Category: Secreted]]
	[[Category: Serine protease]]		[[Category: Serine protease]]
			[[Category: Transferase]]
	[[Category: Transmembrane]]		[[Category: Transmembrane]]
	[[Category: Viral nucleoprotein]]		[[Category: Viral nucleoprotein]]
	[[Category: Virion]]		[[Category: Virion]]
	[[Category: Yellow fever virus]]		[[Category: Yellow fever virus]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:58:48 2010''~~

OCA at 08:49, 22 September 2010

2010-09-22T08:49:50Z

← Older revision		Revision as of 08:49, 22 September 2010
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	3EVD is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Yellow_fever_virus_17d Yellow fever virus 17d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EVD OCA].		3EVD is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Yellow_fever_virus_17d Yellow fever virus 17d]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EVD OCA].

	==Reference==		==Reference==
	~~Analysis of Flavivirus NS5 Methyltransferase Cap Binding., Geiss BJ, Thompson AA, Andrews AJ, Sons RL, Gari HH, Keenan SM, Peersen OB, J Mol Biol. 2008 Dec 11.~~ PMID:~~[http:/~~/~~www.ncbi.nlm.nih.gov~~/~~pubmed/19101564 19101564]~~		<ref group="xtra">PMID:19101564</ref><references group="xtra"/>
	~~[[Category: Single protein]]~~
	[[Category: Yellow fever virus 17d]]		[[Category: Yellow fever virus 17d]]
	[[Category: ~~Pdbx_ordinal=~~, ~~<PDBx~~:~~audit_author~~.]]		[[Category: Geiss, B J.]]
			[[Category: Peersen, O B.]]
			[[Category: Thompson, A A.]]
	[[Category: Atp-binding]]		[[Category: Atp-binding]]
	[[Category: Capsid protein]]		[[Category: Capsid protein]]
Line 56:		Line 57:
	[[Category: Yellow fever virus]]		[[Category: Yellow fever virus]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed ~~Mar 4 20~~:11:~~44 2009~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 22 11:58:48 2010''