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| - | ==crystal structure of yellow fever virus NS3 helicase complexed with ADP==
| + | #REDIRECT [[5ffm]] This PDB entry is obsolete and replaced by 5ffm |
| - | <StructureSection load='1ymf' size='340' side='right' caption='[[1ymf]], [[Resolution|resolution]] 2.60Å' scene=''>
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| - | == Structural highlights ==
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| - | <table><tr><td colspan='2'>[[1ymf]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Flavivirus_febricis Flavivirus febricis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1YMF FirstGlance]. <br>
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| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene></td></tr>
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| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
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| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1yks|1yks]]</td></tr>
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| - | <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=1ymf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ymf OCA], [http://pdbe.org/1ymf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ymf RCSB], [http://www.ebi.ac.uk/pdbsum/1ymf PDBsum]</span></td></tr>
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| - | </table>
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| - | == Function ==
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| - | [[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>
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| - | == Evolutionary Conservation ==
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| - | [[Image:Consurf_key_small.gif|200px|right]]
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| - | Check<jmol>
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| - | <jmolCheckbox>
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| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ym/1ymf_consurf.spt"</scriptWhenChecked>
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| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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| - | <text>to colour the structure by Evolutionary Conservation</text>
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| - | </jmolCheckbox>
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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/chain_selection.php?pdb_ID=2ata ConSurf].
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| - | <div style="clear:both"></div>
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| - | <div style="background-color:#fffaf0;">
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| - | == Publication Abstract from PubMed ==
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| - | Yellow fever virus (YFV), a member of the Flavivirus genus, has a plus-sense RNA genome encoding a single polyprotein. Viral protein NS3 includes a protease and a helicase that are essential to virus replication and to RNA capping. The 1.8-A crystal structure of the helicase region of the YFV NS3 protein includes residues 187 to 623. Two familiar helicase domains bind nucleotide in a triphosphate pocket without base recognition, providing a site for nonspecific hydrolysis of nucleoside triphosphates and RNA triphosphate. The third, C-terminal domain has a unique structure and is proposed to function in RNA and protein recognition. The organization of the three domains indicates that cleavage of the viral polyprotein NS3-NS4A junction occurs in trans.
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| - | Structure of the Flavivirus helicase: implications for catalytic activity, protein interactions, and proteolytic processing.,Wu J, Bera AK, Kuhn RJ, Smith JL J Virol. 2005 Aug;79(16):10268-77. PMID:16051820<ref>PMID:16051820</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 1ymf" style="background-color:#fffaf0;"></div>
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| - | == References ==
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| - | <references/>
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| - | __TOC__
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| - | </StructureSection>
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| - | [[Category: Flavivirus febricis]]
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| - | [[Category: Bera, A K]]
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| - | [[Category: Kuhn, R J]]
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| - | [[Category: Smith, J L]]
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| - | [[Category: Wu, J]]
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| - | [[Category: Adp]]
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| - | [[Category: Atpase]]
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| - | [[Category: Complex]]
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| - | [[Category: Dead-box]]
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| - | [[Category: Flavivirus]]
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| - | [[Category: Helicase]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Rtpase]]
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| - | [[Category: Yellow fever virus]]
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