View source for 6ld3


==Zika NS5 polymerase domain==
<StructureSection load='6ld3' size='340' side='right'caption='[[6ld3]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6ld3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Zika_virus_ZIKV/H._sapiens/FrenchPolynesia/10087PF/2013 Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LD3 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]] 2.3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FB2:BENZENESULFONAMIDE'>FB2</scene>, <scene name='pdbligand=G8O:2,4-dimethoxy-5-thiophen-2-yl-benzoic+acid'>G8O</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=6ld3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ld3 OCA], [https://pdbe.org/6ld3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ld3 RCSB], [https://www.ebi.ac.uk/pdbsum/6ld3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ld3 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/POLG_ZIKVF POLG_ZIKVF] Capsid protein C: Plays a role in virus budding by binding to the cell membrane and gathering the viral RNA into a nucleocapsid that forms the core of a mature virus particle. During virus entry, may induce genome penetration into the host cytoplasm after hemifusion induced by the surface proteins. Can migrate to the cell nucleus where it modulates host functions.[UniProtKB:P17763]  Capsid protein C: Inhibits RNA silencing by interfering with host Dicer.[UniProtKB:P03314]  Peptide pr: Prevents premature fusion activity of envelope proteins in trans-Golgi by binding to envelope protein E at pH6.0. After virion release in extracellular space, gets dissociated from E dimers.[UniProtKB:P17763]  Protein prM: Plays a role in host immune defense modulation and protection of envelope protein E during virion synthesis. PrM-E cleavage is ineficient, and immature prM-E proteins could have an activity against host immune response. The sequence of PrM contributes to fetal microcephaly in Humans. Acts as a chaperone for envelope protein E during intracellular virion assembly by masking and inactivating envelope protein E fusion peptide. prM is the only viral peptide matured by host furin in the trans-Golgi network probably to avoid catastrophic activation of the viral fusion activity in acidic Golgi compartment prior to virion release. prM-E cleavage is inefficient, and many virions are only partially matured. These uncleaved prM could play a role in immune evasion.[UniProtKB:P17763]<ref>PMID:28971967</ref>   Small envelope protein M: May play a role in virus budding. Exerts cytotoxic effects by activating a mitochondrial apoptotic pathway through M ectodomain. May display a viroporin activity.[UniProtKB:P17763]  Envelope protein E: Binds to host cell surface receptor and mediates fusion between viral and cellular membranes. Envelope protein is synthesized in the endoplasmic reticulum in the form of heterodimer with protein prM. They play a role in virion budding in the ER, and the newly formed immature particule is covered with 60 spikes composed of heterodimer between precursor prM and envelope protein E. The virion is transported to the Golgi apparatus where the low pH causes dissociation of PrM-E heterodimers and formation of E homodimers. prM-E cleavage is inefficient, and many virions are only partially matured. These uncleaved prM could play a role in immune evasion.[UniProtKB:P17763]  Non-structural protein 1: Involved in immune evasion, pathogenesis and viral replication. Once cleaved off the polyprotein, is targeted to three destinations: the viral replication cycle, the plasma membrane and the extracellular compartment. Essential for viral replication. Required for formation of the replication complex and recruitment of other non-structural proteins to the ER-derived membrane structures. Excreted as a hexameric lipoparticle that plays a role against host immune response. Antagonizing the complement function. Binds to the host macrophages and dendritic cells. Inhibits signal transduction originating from Toll-like receptor 3 (TLR3).[UniProtKB:Q9Q6P4]  Non-structural protein 2A: Component of the viral RNA replication complex that functions in virion assembly and antagonizes the host alpha/beta interferon antiviral response (By similarity). Disrupts adherens junction formation and thereby impairs proliferation of radial cells in both embryonic mouse cortex and human forebrain organoids (PubMed:28826723).[UniProtKB:P14335]<ref>PMID:28826723</ref>   Non-structural protein 2B: Required cofactor for the serine protease function of NS3.[UniProtKB:Q32ZE1]  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). Leads to translation arrest when expressed ex vivo (PubMed:28592527).[UniProtKB:Q32ZE1]<ref>PMID:28592527</ref>   Non-structural protein 4A: Regulates the ATPase activity of the NS3 helicase activity. NS4A allows NS3 helicase to conserve energy during unwinding (By similarity). Cooperatively with NS4B suppress the Akt-mTOR pathway and lead to cellular dysregulation (PubMed:27524440). Leads to translation arrest when expressed ex vivo (PubMed:28592527).[UniProtKB:Q9Q6P4]<ref>PMID:27524440</ref> <ref>PMID:28592527</ref>   Peptide 2k: Functions as a signal peptide for NS4B and is required for the interferon antagonism activity of the latter.  Non-structural protein 4B: Induces the formation of ER-derived membrane vesicles where the viral replication takes place. 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. Inhibits STAT2 translocation in the nucleus after IFN-alpha treatment (By similarity). Cooperatively with NS4A suppress the Akt-mTOR pathway and lead to cellular dysregulation (PubMed:27524440).[UniProtKB:Q9Q6P4]<ref>PMID:27524440</ref>   RNA-directed RNA polymerase NS5: Replicates the viral (+) and (-) RNA 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 RNA genome replication, also prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) signaling pathway. Inhibits host TYK2 and STAT2 phosphorylation, thereby preventing activation of JAK-STAT signaling pathway.[UniProtKB:Q9Q6P4]
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== Publication Abstract from PubMed ==
Zika virus (ZIKV) remains a potentially significant public health concern because it can cause teratogenic effects such as microcephaly in newborns and neurological disease like Guillain-Barre syndrome. Together with efforts to develop a vaccine, the discovery of antiviral molecules is important to control ZIKV infections and to prevent its most severe symptoms. Here we report the development of small non-nucleoside inhibitors (NNIs) of ZIKV RNA-dependent RNA polymerase (RdRp) activity. These NNIs target an allosteric pocket ("N-pocket") located next to a putative hinge region between the thumb and the palm subdomains, that was originally described for dengue virus (DENV) RdRp. We first tested DENV RdRp N-pocket inhibitors against ZIKV RdRp, introduced chemical modifications into these molecules and assessed their potency using both enzymatic and cell-based assays. The most potent compound has an IC50 value of 7.3 muM and inhibits ZIKV replication in a cell-based assay with an EC50 value of 24.3 muM. Importantly we report four high-resolution crystal structures detailing how these NNIs insert into the N-pocket of ZIKV RdRp. Our observations point to subtle differences in the size, shape, chemical environment and hydration of the N-pocket from ZIKV RdRp compared to DENV RdRp, that are crucial for the design of improved antiviral inhibitors against ZIKV.IMPORTANCE Zika virus belongs to the flavivirus family that comprises several important human pathogens. There is currently neither an approved vaccine nor antiviral drugs available to prevent infection by ZIKV. The NS5 polymerase, which is responsible for replicating the viral RNA genome, represents one of the most promising targets for antiviral drug development. Starting from compounds recently developed against dengue virus NS5, we designed and synthetized inhibitors targeting the Zika virus NS5. We showed that these novel compounds inhibit viral replication by targeting the polymerase activity. High-resolution X-ray crystallographic structures of protein-inhibitor complexes demonstrate specific binding to an allosteric site within the polymerase called the N-pocket. This work paves the way for future structure-based design of potent compounds specifically targeting the ZIKV RNA polymerase activity.

Non-Nucleoside Inhibitors of Zika virus RNA-dependent RNA polymerase.,Gharbi-Ayachi A, Santhanakrishnan S, Wong YH, Chan KWK, Tan ST, Bates RW, Vasudevan SG, El Sahili A, Lescar J J Virol. 2020 Aug 12. pii: JVI.00794-20. doi: 10.1128/JVI.00794-20. PMID:32796069<ref>PMID:32796069</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 6ld3" style="background-color:#fffaf0;"></div>

==See Also==
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013]]
[[Category: El Sahili A]]
[[Category: Lescar J]]