View source for 6qsn


==Crystal structure of Yellow fever virus polymerase NS5A==
<StructureSection load='6qsn' size='340' side='right'caption='[[6qsn]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6qsn]] is a 2 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=6QSN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QSN FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.004&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SAH:S-ADENOSYL-L-HOMOCYSTEINE'>SAH</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=6qsn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qsn OCA], [https://pdbe.org/6qsn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qsn RCSB], [https://www.ebi.ac.uk/pdbsum/6qsn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qsn ProSAT]</span></td></tr>
</table>
== Function ==
[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> 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Yellow fever virus (YFV) is responsible for devastating outbreaks of Yellow fever (YF) in humans and is associated with high mortality rates. Recent large epidemics and epizootics and exponential increases in the numbers of YF cases in humans and non-human primates highlight the increasing threat YFV poses, despite the availability of an effective YFV vaccine. YFV is the first human virus discovered, but the structures of several of the viral proteins remain poorly understood. Here we report the structure of the full-length NS5 protein, a key enzyme for the replication of flaviviruses that contains both a methyltransferase domain and an RNA dependent RNA polymerase domain, at 3.1A resolution. The viral polymerase adopts right-hand fold, demonstrating the similarities of the Yellow fever, Dengue and Zika polymerases. Together this data suggests NS5 as a prime and ideal target for the design of pan-flavivirus inhibitors.

Structure of the yellow fever NS5 protein reveals conserved drug targets shared among flaviviruses.,Dubankova A, Boura E Antiviral Res. 2019 Sep;169:104536. doi: 10.1016/j.antiviral.2019.104536. Epub, 2019 Jun 13. PMID:31202975<ref>PMID:31202975</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 6qsn" style="background-color:#fffaf0;"></div>

==See Also==
*[[Nonstructural protein 3D structures|Nonstructural protein 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Yellow fever virus 17D]]
[[Category: Boura E]]
[[Category: Dubankova A]]