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- PDB-3zd0: The Solution Structure of Monomeric Hepatitis C Virus p7 Yields P... -

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Entry
Database: PDB / ID: 3zd0
TitleThe Solution Structure of Monomeric Hepatitis C Virus p7 Yields Potent Inhibitors of Virion Release
ComponentsP7 PROTEIN
KeywordsTRANSPORT PROTEIN / ANTIVIRAL / ION CHANNEL / VIROPORIN
Function / homology
Function and homology information


host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated transformation of host cell / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / channel activity / viral nucleocapsid ...host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / symbiont-mediated transformation of host cell / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / ribonucleoside triphosphate phosphatase activity / channel activity / viral nucleocapsid / monoatomic ion transmembrane transport / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / ribonucleoprotein complex / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : ...Hepatitus C virus, Non-structural 5a protein, C-terminal / Hepatitis C virus NS5A, 1B domain superfamily / Hepatitis C virus non-structural protein NS2, C-terminal domain / Hepatitis C virus non-structural protein NS2, N-terminal domain / Hepatitis C virus non-structural protein NS2 / HCV NS5a protein C-terminal region / Hepatitis C virus, Non-structural protein NS4b / Hepatitis C virus, Core protein, N-terminal / Hepatitis C virus core protein, chain A superfamily / : / Hepatitis C virus non-structural protein NS4b / Hepatitis C virus capsid protein / Hepatitis C virus, Non-structural protein NS2 / Hepatitis C virus, Non-structural 5a protein / Hepatitis C virus, Non-structural 5a protein, domain 1a / Hepatitis C virus non-structural 5a, 1B domain / NS5A domain 1a superfamily / : / Hepatitis C virus non-structural 5a protein membrane anchor / Hepatitis C virus non-structural 5a zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus, Non-structural protein NS4a / Hepatitis C virus non-structural protein NS4a / Hepatitis C virus, Core protein, C-terminal / Hepatitis C virus core protein / Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1 / RNA dependent RNA polymerase, hepatitis C virus / Viral RNA dependent RNA polymerase / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / DEAD box, Flavivirus / Flavivirus DEAD domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHEPATITIS C VIRUS
MethodSOLUTION NMR / ARIA MEMBRANE CS ROSETTA
AuthorsFoster, T.L. / Sthompson, G. / Kalverda, A.P. / Kankanala, J. / Thompson, J. / Barker, A.M. / Clarke, D. / Noerenberg, M. / Pearson, A.R. / Rowlands, D.J. ...Foster, T.L. / Sthompson, G. / Kalverda, A.P. / Kankanala, J. / Thompson, J. / Barker, A.M. / Clarke, D. / Noerenberg, M. / Pearson, A.R. / Rowlands, D.J. / Homans, S.W. / Harris, M. / Foster, R. / Griffin, S.D.C.
Citation
Journal: Hepatology / Year: 2014
Title: Structure-Guided Design Affirms Inhibitors of Hepatitis C Virus P7 as a Viable Class of Antivirals Targeting Virion Release
Authors: Foster, T.L. / Thompson, G.S. / Kalverda, A.P. / Kankanala, J. / Bentham, M. / Wetherill, L.F. / Thompson, J. / Barker, A.M. / Clarke, D. / Noerenberg, M. / Pearson, A.R. / Rowlands, D.J. / ...Authors: Foster, T.L. / Thompson, G.S. / Kalverda, A.P. / Kankanala, J. / Bentham, M. / Wetherill, L.F. / Thompson, J. / Barker, A.M. / Clarke, D. / Noerenberg, M. / Pearson, A.R. / Rowlands, D.J. / Homans, S.W. / Harris, M. / Foster, R. / Griffin, S.D.C.
#1: Journal: Ph D Thesis / Year: 2010
Title: Structural and Functional Characterisation of the Hepititis C Virus Proteins P7, Ns2-3 and Ns5A
Authors: Foster, T.L.
History
DepositionNov 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Feb 12, 2014Group: Database references
Revision 2.0Sep 25, 2019Group: Atomic model / Data collection / Other
Category: atom_site / pdbx_database_status / pdbx_nmr_software
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 2.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 2.2Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P7 PROTEIN


Theoretical massNumber of molelcules
Total (without water)9,0651
Polymers9,0651
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30ENERGY
RepresentativeModel #1

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Components

#1: Protein P7 PROTEIN


Mass: 9065.472 Da / Num. of mol.: 1 / Fragment: RESIDUES 747-809
Source method: isolated from a genetically manipulated source
Details: FLAG TAG AT RESIDUES UPTO AND INCLUDING RESIDUE 18 / Source: (gene. exp.) HEPATITIS C VIRUS / Strain: 1B / Variant: J4 ISOLATE / Plasmid: PGEX-FLAGP7(J4) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WLK8

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C HSQC HCCARO
12115N HSQC
131HNCA
141HN(CO)CA
151H(CCO)NH
161HCCACONH
171(HB)CB(CGCD)HD
181(H)CCH TOCSY
191(H)CCH COSY
1101HN(CA)CB
1111CBCA(CO)NH
1121HCCHTOCSY
1131HNHA
114115N HSQC NOESY
11512D HH NOESY
11612D HH TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED FLAG-P7. STRUCTURES ARE FROM MEMBRANE CS ROSETTA REFINED WITH NOES IN ARIA 2

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Sample preparation

DetailsContents: METHANOL
Sample conditionsPressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
MEMBRANE CS ROSETTA, ARIA 2.2U3, CNS2.2U3,CNSSHEN,VERNON,BAKER,BAX,RIEPLING,HABECK, BARDIAUX,BERNARD,MALLIAVIN,NILGES,BRUNGER, ADAMS,CLORE,DELANO,GROS,GROSSE-KUNSTLEVE, JIANG,KUSZEWSKI,NILGES,PANNU,READ,RICE, SIMONSON,WARRENrefinement
CcpNmr Analysis1.15structure solution
CcpNmr Analysis2.2structure solution
TALOS2007.068.09.0structure solution
CNS1.1structure solution
CS-ROSETTA1.01structure solution
Rosetta3structure solution
ARIA2.2U3structure solution
RefinementMethod: ARIA MEMBRANE CS ROSETTA / Software ordinal: 1
Details: REFINED FROM AN INITAL TEMPLATE STRUCTURE FROM CS MEMBRANE ROSETTA ALL NOES ASSIGNED AUTOMATICALLY
NMR ensembleConformer selection criteria: ENERGY / Conformers calculated total number: 30 / Conformers submitted total number: 20

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