2f9v: Difference between revisions

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-{{Seed}}
-[[Image:2f9v.png|left|200px]]
-<!--
+==HCV NS3 protease domain with NS4a peptide and a ketoamide inhibitor with P1 and P2 cyclopropylalannines==
-The line below this paragraph, containing "STRUCTURE_2f9v", creates the "Structure Box" on the page.
+<StructureSection load='2f9v' size='340' side='right'caption='[[2f9v]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2f9v]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Hepacivirus_hominis Hepacivirus hominis] and [https://en.wikipedia.org/wiki/Hepatitis_C_virus_(isolate_H) Hepatitis C virus (isolate H)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2F9V FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BN6:(2S,8R,9S,15S)-15-CYCLOHEXYL-9,12-BIS(CYCLOPROPYLMETHYL)-8-HYDROXY-20-METHYL-4,7,11,14,17-PENTAOXO-2-PHENYL-18-OXA-3,6,10,12,13,16-HEXAAZAHENICOSAN-1-OIC+ACID'>BN6</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2f9v|  PDB=2f9v  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2f9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2f9v OCA], [https://pdbe.org/2f9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2f9v RCSB], [https://www.ebi.ac.uk/pdbsum/2f9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2f9v ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/POLG_HCV77 POLG_HCV77] Packages viral RNA to form a viral nucleocapsid, and promotes virion budding (Probable). Participates in the viral particle production as a result of its interaction with the non-structural protein 5A (By similarity). Binds RNA and may function as a RNA chaperone to induce the RNA structural rearrangements taking place during virus replication (PubMed:18033802). Modulates viral translation initiation by interacting with viral IRES and 40S ribosomal subunit (By similarity). Affects various cell signaling pathways, host immunity and lipid metabolism (Probable). Prevents the establishment of cellular antiviral state by blocking the interferon-alpha/beta (IFN-alpha/beta) and IFN-gamma signaling pathways and by blocking the formation of phosphorylated STAT1 and promoting ubiquitin-mediated proteasome-dependent degradation of STAT1 (By similarity) (PubMed:23799612). Activates STAT3 leading to cellular transformation (By similarity). Regulates the activity of cellular genes, including c-myc and c-fos (By similarity). May repress the promoter of p53, and sequester CREB3 and SP110 isoform 3/Sp110b in the cytoplasm (By similarity). Represses cell cycle negative regulating factor CDKN1A, thereby interrupting an important check point of normal cell cycle regulation (By similarity). Targets transcription factors involved in the regulation of inflammatory responses and in the immune response: suppresses NF-kappa-B activation, and activates AP-1 (By similarity). Binds to dendritic cells (DCs) via C1QR1, resulting in down-regulation of T-lymphocytes proliferation (PubMed:11086025, PubMed:17881511). Alters lipid metabolism by interacting with hepatocellular proteins involved in lipid accumulation and storage (PubMed:14602201). Induces up-regulation of FAS promoter activity, and thereby contributes to the increased triglyceride accumulation in hepatocytes (steatosis) (PubMed:14602201).[UniProtKB:P26662][UniProtKB:P26664][UniProtKB:P29846][UniProtKB:Q99IB8]<ref>PMID:11086025</ref> <ref>PMID:14602201</ref> <ref>PMID:17881511</ref> <ref>PMID:18033802</ref> <ref>PMID:23799612</ref>   Forms a heterodimer with envelope glycoprotein E2, which mediates virus attachment to the host cell, virion internalization through clathrin-dependent endocytosis and fusion with host membrane (PubMed:14990718, PubMed:16894197). Fusion with the host cell is most likely mediated by both E1 and E2, through conformational rearrangements of the heterodimer required for fusion rather than a classical class II fusion mechanism (PubMed:16533059, PubMed:24698129, PubMed:29505618). E1/E2 heterodimer binds host apolipoproteins such as APOB and APOE thereby forming a lipo-viro-particle (LVP) (PubMed:24838241, PubMed:25122793, PubMed:29695434). APOE associated to the LVP allows the initial virus attachment to cell surface receptors such as the heparan sulfate proteoglycans (HSPGs), syndecan-1 (SDC1), syndecan-1 (SDC2), the low-density lipoprotein receptor (LDLR) and scavenger receptor class B type I (SCARB1) (PubMed:12356718, PubMed:12913001, PubMed:12970454, PubMed:22767607, PubMed:28404852). The cholesterol transfer activity of SCARB1 allows E2 exposure and binding of E2 to SCARB1 and the tetraspanin CD81 (PubMed:12913001, PubMed:22767607). E1/E2 heterodimer binding on CD81 activates the epithelial growth factor receptor (EGFR) signaling pathway (PubMed:22855500). Diffusion of the complex E1/E2-EGFR-SCARB1-CD81 to the cell lateral membrane allows further interaction with Claudin 1 (CLDN1) and occludin (OCLN) to finally trigger HCV entry (By similarity) (PubMed:12913001, PubMed:12970454, PubMed:19182773, PubMed:20375010, PubMed:24038151).[UniProtKB:Q99IB8]<ref>PMID:12356718</ref> <ref>PMID:12913001</ref> <ref>PMID:12970454</ref> <ref>PMID:14990718</ref> <ref>PMID:16533059</ref> <ref>PMID:16894197</ref> <ref>PMID:19182773</ref> <ref>PMID:20375010</ref> <ref>PMID:22767607</ref> <ref>PMID:22855500</ref> <ref>PMID:24038151</ref> <ref>PMID:24698129</ref> <ref>PMID:24838241</ref> <ref>PMID:25122793</ref> <ref>PMID:28404852</ref> <ref>PMID:29505618</ref> <ref>PMID:29695434</ref>   Forms a heterodimer with envelope glycoprotein E1, which mediates virus attachment to the host cell, virion internalization through clathrin-dependent endocytosis and fusion with host membrane (PubMed:14990718, PubMed:16894197). Fusion with the host cell is most likely mediated by both E1 and E2, through conformational rearrangements of the heterodimer required for fusion rather than a classical class II fusion mechanism (PubMed:16533059, PubMed:24698129, PubMed:29505618). The interaction between E2 and host apolipoprotein E/APOE allows the proper assembly, maturation and infectivity of the viral particles (PubMed:25122793, PubMed:29695434). This interaction is probably promoted via the up-regulation of cellular autophagy by the virus (PubMed:29695434). E1/E2 heterodimer binds host apolipoproteins such as APOB and APOE thereby forming a lipo-viro-particle (LVP) (PubMed:24838241, PubMed:25122793, PubMed:29695434). APOE associated to the LVP allows the initial virus attachment to cell surface receptors such as the heparan sulfate proteoglycans (HSPGs), syndecan-1 (SDC1), syndecan-1 (SDC2), the low-density lipoprotein receptor (LDLR) and scavenger receptor class B type I (SCARB1) (PubMed:12356718, PubMed:12913001, PubMed:12970454, PubMed:22767607, PubMed:28404852). The cholesterol transfer activity of SCARB1 allows E2 exposure and binding of E2 to SCARB1 and the tetraspanin CD81 (PubMed:12913001, PubMed:22767607). E1/E2 heterodimer binding on CD81 activates the epithelial growth factor receptor (EGFR) signaling pathway (By similarity) (PubMed:12913001, PubMed:12970454, PubMed:19182773, PubMed:20375010, PubMed:22855500, PubMed:24038151). Diffusion of the complex E1/E2-EGFR-SCARB1-CD81 to the cell lateral membrane allows further interaction with Claudin 1 (CLDN1) and occludin (OCLN) to finally trigger HCV entry (By similarity) (PubMed:12913001, PubMed:12970454, PubMed:19182773, PubMed:20375010, PubMed:24038151). Inhibits host EIF2AK2/PKR activation, preventing the establishment of an antiviral state (By similarity). Viral ligand for CD209/DC-SIGN and CLEC4M/DC-SIGNR, which are respectively found on DCs, and on liver sinusoidal endothelial cells and macrophage-like cells of lymph node sinuses (PubMed:15371595). These interactions allow the capture of circulating HCV particles by these cells and subsequent facilitated transmission to permissive cells such as hepatocytes and lymphocyte subpopulations (PubMed:15371595). The interaction between E2 and host amino acid transporter complex formed by SLC3A2 and SLC7A5/LAT1 may facilitate viral entry into host cell (PubMed:30341327).[UniProtKB:P26664][UniProtKB:Q99IB8]<ref>PMID:12356718</ref> <ref>PMID:12913001</ref> <ref>PMID:12970454</ref> <ref>PMID:14990718</ref> <ref>PMID:15371595</ref> <ref>PMID:16533059</ref> <ref>PMID:16894197</ref> <ref>PMID:19182773</ref> <ref>PMID:20375010</ref> <ref>PMID:22767607</ref> <ref>PMID:22855500</ref> <ref>PMID:24038151</ref> <ref>PMID:24698129</ref> <ref>PMID:24838241</ref> <ref>PMID:25122793</ref> <ref>PMID:28404852</ref> <ref>PMID:29505618</ref> <ref>PMID:29695434</ref> <ref>PMID:30341327</ref>   Ion channel protein that acts as a viroporin and plays an essential role in the assembly, envelopment and secretion of viral particles (PubMed:12719519, PubMed:20824094, PubMed:27320856). Participates in virus envelopment by coordinating the encounter between NS5A and NS2-based assembly sites loaded with E1/E2 heterodimer, which subsequently leads to nucleocapsid envelopment (By similarity). Creates a pore in acidic organelles and releases Ca(2+) and H(+) in the cytoplasm of infected cells, leading to a productive viral infection (Probable) (PubMed:20824094). High levels of cytoplasmic Ca(2+) may trigger membrane trafficking and transport of viral ER-associated proteins to viroplasms, sites of viral genome replication (Probable). The release of Ca(2+) may also activate the inflamasome leading to chronic inflammation (Probable) (PubMed:31801866). Targets also host mitochondria and induces mitochondrial depolarization (PubMed:29039530). In addition of its role as a viroporin, acts as a lipid raft adhesion factor (PubMed:27320856).[UniProtKB:Q99IB8]<ref>PMID:12719519</ref> <ref>PMID:20824094</ref> <ref>PMID:27320856</ref> <ref>PMID:29039530</ref> <ref>PMID:31801866</ref> <ref>PMID:14741348</ref> <ref>PMID:24006444</ref>   Cysteine protease required for the proteolytic auto-cleavage between the non-structural proteins NS2 and NS3 (PubMed:8248148). The N-terminus of NS3 is required for the function of NS2 protease (active region NS2-3) (By similarity). Promotes the initiation of viral particle assembly by mediating the interaction between structural and non-structural proteins (PubMed:21147927).[UniProtKB:P26663]<ref>PMID:21147927</ref> <ref>PMID:8248148</ref>   Displays three enzymatic activities: serine protease with a chymotrypsin-like fold, NTPase and RNA helicase (PubMed:25551442). NS3 serine protease, in association with NS4A, is responsible for the cleavages of NS3-NS4A, NS4A-NS4B, NS4B-NS5A and NS5A-NS5B (PubMed:8035505, PubMed:8189513, PubMed:8386278). The NS3/NS4A complex prevents phosphorylation of host IRF3, thus preventing the establishment of dsRNA induced antiviral state (By similarity). The NS3/NS4A complex induces host amino acid transporter component SLC3A2, thus contributing to HCV propagation (PubMed:30341327). NS3 RNA helicase binds to RNA and unwinds both dsDNA and dsRNA in the 3' to 5' direction, and likely resolves RNA complicated stable secondary structures in the template strand (Probable). Binds a single ATP and catalyzes the unzipping of a single base pair of dsRNA (PubMed:21940894). Inhibits host antiviral proteins TBK1 and IRF3 thereby preventing the establishment of an antiviral state (By similarity). Cleaves host MAVS/CARDIF thereby preventing the establishment of an antiviral state (PubMed:16177806, PubMed:16301520). Cleaves host TICAM1/TRIF, thereby disrupting TLR3 signaling and preventing the establishment of an antiviral state (PubMed:15710891).[UniProtKB:Q9WMX2]<ref>PMID:15710891</ref> <ref>PMID:16177806</ref> <ref>PMID:16301520</ref> <ref>PMID:21940894</ref> <ref>PMID:25551442</ref> <ref>PMID:30341327</ref> <ref>PMID:8035505</ref> <ref>PMID:8189513</ref> <ref>PMID:8386278</ref> <ref>PMID:15269774</ref>   Peptide cofactor which forms a non-covalent complex with the N-terminal of NS3 serine protease (PubMed:21507982, PubMed:8189513). The NS3/NS4A complex prevents phosphorylation of host IRF3, thus preventing the establishment of dsRNA induced antiviral state (By similarity). The NS3/NS4A complex induces host amino acid transporter component SLC3A2, thus contributing to HCV propagation (PubMed:30341327).[UniProtKB:Q9WMX2]<ref>PMID:21507982</ref> <ref>PMID:30341327</ref> <ref>PMID:8189513</ref>   Induces a specific membrane alteration that serves as a scaffold for the virus replication complex (PubMed:12021330). This membrane alteration gives rise to the so-called ER-derived membranous web that contains the replication complex (PubMed:12021330). NS4B self-interaction contributes to its function in membranous web formation (PubMed:16731940). Promotes host TRIF protein degradation in a CASP8-dependent manner thereby inhibiting host TLR3-mediated interferon signaling (PubMed:29782532). Disrupts the interaction between STING and TBK1 contributing to the inhibition of interferon signaling (PubMed:23542348).<ref>PMID:12021330</ref> <ref>PMID:16731940</ref> <ref>PMID:23542348</ref> <ref>PMID:29782532</ref>   Phosphorylated protein that is indispensable for viral replication and assembly (PubMed:27578425). Both hypo- and hyperphosphorylated states are required for the viral life cycle (By similarity). The hyperphosphorylated form of NS5A is an inhibitor of viral replication (By similarity). Involved in RNA-binding and especially in binding to the viral genome (Probable). Zinc is essential for RNA-binding (PubMed:20926572). Participates in the viral particle production as a result of its interaction with the viral mature core protein (By similarity). Its interaction with host VAPB may target the viral replication complex to vesicles (By similarity). Down-regulates viral IRES translation initiation (By similarity). Mediates interferon resistance, presumably by interacting with and inhibiting host EIF2AK2/PKR (PubMed:16951545). Prevents BIN1-induced apoptosis (PubMed:16530520). Acts as a transcriptional activator of some host genes important for viral replication when localized in the nucleus (By similarity). Via the interaction with host PACSIN2, modulates lipid droplet formation in order to promote virion assembly (PubMed:31801866). Modulates TNFRSF21/DR6 signaling pathway for viral propagation (PubMed:28743875).[UniProtKB:P26662][UniProtKB:P26664][UniProtKB:Q99IB8][UniProtKB:Q9WMX2]<ref>PMID:16530520</ref> <ref>PMID:16951545</ref> <ref>PMID:20926572</ref> <ref>PMID:25683609</ref> <ref>PMID:27578425</ref> <ref>PMID:28743875</ref> <ref>PMID:31801866</ref> <ref>PMID:20926572</ref>   RNA-dependent RNA polymerase that performs primer-template recognition and RNA synthesis during viral replication (PubMed:20729191). Initiates RNA transcription/replication at a flavin adenine dinucleotide (FAD), resulting in a 5'- FAD cap on viral RNAs. In this way, recognition of viral 5' RNA by host pattern recognition receptors can be bypassed (PubMed:37407817), thereby evading activation of antiviral pathways.<ref>PMID:20729191</ref> <ref>PMID:37407817</ref>
+== 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/f9/2f9v_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=2f9v ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Depeptidization efforts of the P(3)-P(2) region of P(3) capped alpha-ketoamide inhibitor of HCV NS3 serine protease 1 are reported. We clearly established that N-methylation of the P(2) nitrogen and modification of the P(2)' carboxylic acid terminus were essential for activity in the replicon assay.
-===HCV NS3 protease domain with NS4a peptide and a ketoamide inhibitor with P1 and P2 cyclopropylalannines===
+Depeptidization efforts on P3-P2' alpha-ketoamide inhibitors of HCV NS3-4A serine protease: effect on HCV replicon activity.,Bogen SL, Ruan S, Liu R, Agrawal S, Pichardo J, Prongay A, Baroudy B, Saksena AK, Girijavallabhan V, Njoroge FG Bioorg Med Chem Lett. 2006 Mar 15;16(6):1621-7. Epub 2006 Jan 4. PMID:16387495<ref>PMID:16387495</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2f9v" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16387495}}, adds the Publication Abstract to the page
+*[[Helicase 3D structures|Helicase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16387495 is the PubMed ID number.
+*[[Virus protease 3D structures|Virus protease 3D structures]]
--->
+== References ==
-{{ABSTRACT_PUBMED_16387495}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-F9V is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Hepatitis_c_virus Hepatitis c virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2F9V OCA].
+[[Category: Hepacivirus hominis]]
+[[Category: Large Structures]]
-==Reference==
+[[Category: Agrawal S]]
-Depeptidization efforts on P3-P2' alpha-ketoamide inhibitors of HCV NS3-4A serine protease: effect on HCV replicon activity., Bogen SL, Ruan S, Liu R, Agrawal S, Pichardo J, Prongay A, Baroudy B, Saksena AK, Girijavallabhan V, Njoroge FG, Bioorg Med Chem Lett. 2006 Mar 15;16(6):1621-7. Epub 2006 Jan 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16387495 16387495]
+[[Category: Baroudy B]]
+[[Category: Bogen SL]]
-Crystal structure of the hepatitis C virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide., Kim JL, Morgenstern KA, Lin C, Fox T, Dwyer MD, Landro JA, Chambers SP, Markland W, Lepre CA, O'Malley ET, Harbeson SL, Rice CM, Murcko MA, Caron PR, Thomson JA, Cell. 1996 Oct 18;87(2):343-55. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8861917 8861917]
+[[Category: Girijavallabhan V]]
+[[Category: Liu R]]
-Hepatitis C virus NS3-4A serine protease inhibitors: use of a P2-P1 cyclopropyl alanine combination for improved potency., Bogen S, Saksena AK, Arasappan A, Gu H, Njoroge FG, Girijavallabhan V, Pichardo J, Butkiewicz N, Prongay A, Madison V, Bioorg Med Chem Lett. 2005 Oct 15;15(20):4515-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16112862 16112862]
+[[Category: Njoroge FG]]
+[[Category: Pichardo J]]
-Design and synthesis of depeptidized macrocyclic inhibitors of hepatitis C NS3-4A protease using structure-based drug design., Venkatraman S, Njoroge FG, Girijavallabhan VM, Madison VS, Yao NH, Prongay AJ, Butkiewicz N, Pichardo J, J Med Chem. 2005 Aug 11;48(16):5088-91. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16078825 16078825]
+[[Category: Prongay A]]
+[[Category: Ruan S]]
-Proline-based macrocyclic inhibitors of the hepatitis C virus: stereoselective synthesis and biological activity., Chen KX, Njoroge FG, Vibulbhan B, Prongay A, Pichardo J, Madison V, Buevich A, Chan TM, Angew Chem Int Ed Engl. 2005 Nov 4;44(43):7024-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16211639 16211639]
+[[Category: Saksena A]]
-Novel 2-oxoimidazolidine-4-carboxylic acid derivatives as hepatitis C virus NS3-4A serine protease inhibitors: synthesis, activity, and X-ray crystal structure of an enzyme inhibitor complex., Arasappan A, Njoroge FG, Parekh TN, Yang X, Pichardo J, Butkiewicz N, Prongay A, Yao N, Girijavallabhan V, Bioorg Med Chem Lett. 2004 Dec 6;14(23):5751-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15501035 15501035]
-[[Category: Hepatitis c virus]]
-[[Category: Protein complex]]
-[[Category: Agrawal, S.]]
-[[Category: Baroudy, B.]]
-[[Category: Bogen, S L.]]
-[[Category: Girijavallabhan, V.]]
-[[Category: Liu, R.]]
-[[Category: Njoroge, F G.]]
-[[Category: Pichardo, J.]]
-[[Category: Prongay, A.]]
-[[Category: Ruan, S.]]
-[[Category: Saksena, A.]]
-[[Category: Hcv]]
-[[Category: Hepatitis c protease]]
-[[Category: Ketoamide inhibitor]]
-[[Category: Ns3 protease]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 20:39:28 2008''