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- PDB-2m6x: Structure of the p7 channel of Hepatitis C virus, genotype 5a -

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Basic information

Entry
Database: PDB / ID: 2m6x
TitleStructure of the p7 channel of Hepatitis C virus, genotype 5a
Componentsp7
KeywordsMEMBRANE PROTEIN / cation channel
Function / homology
Function and homology information


symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / : / : / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 ...symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / : / : / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / SH3 domain binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / 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 / RNA helicase / induction by virus of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / RNA binding / zinc ion binding / extracellular region / ATP binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1750 / 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 non-structural protein NS4b ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1750 / 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 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 / 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. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 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 / simulated annealing, molecular dynamics
Model detailslowest energy, model1
AuthorsOuYang, B. / Chou, J.J.
CitationJournal: Nature / Year: 2013
Title: Unusual architecture of the p7 channel from hepatitis C virus
Authors: OuYang, B. / Xie, S. / Berardi, M.J. / Zhao, X. / Dev, J. / Yu, W. / Sun, B. / Chou, J.J.
History
DepositionApr 12, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 12, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: p7
B: p7
C: p7
D: p7
E: p7
F: p7


Theoretical massNumber of molelcules
Total (without water)40,5726
Polymers40,5726
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 60structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein
p7


Mass: 6762.074 Da / Num. of mol.: 6 / Mutation: T1G, A12S, C2A, C27T, C44S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Strain: EUH1480 / Variant: genotype 5a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: O39928

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HNCA
1213D HN(CO)CA
1313D HN(CA)CO
1413D HNCO
1513D HN(CA)CB
1613D HN(COCA)CB
1723D 1H-15N NOESY
1823D 1H-13C NOESY (MET)
1923D 1H-13C NOESY (Diag Suppress)
11043D 1H-15N NOESY (mixed NOE)
11132D 1H-15N HSQC (28m CT)
1125J-scaled 15N TROSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N; U-80% 2H] HCV p7 (monomer)-1, 200 mM DPC-2, 25 mM MES-3, 95% H2O/5% D2O95% H2O/5% D2O
20.8 mM [U-100% 13C; U-100% 15N] HCV p7 (monomer)-4, 200 mM [U-2H] DPC-5, 25 mM MES-6, 95% H2O/5% D2O95% H2O/5% D2O
30.8 mM [U-15% 13C] HCV p7 (monomer)-7, 200 mM [U-2H] DPC-8, 25 mM MES-9, 95% H2O/5% D2O95% H2O/5% D2O
40.4 mM [U-15N; U-2H] HCV p7 (monomer)-10, 0.4 mM [U-13C] HCV p7 (monomer)-11, 200 mM [U-2H] DPC-12, 25 mM MES-13, 95% H2O/5% D2O95% H2O/5% D2O
50.2 mM [U-100% 13C; U-100% 15N; U-80% 2H] HCV p7 (monomer)-14, 100 mM DPC-15, 25 mM MES-16, 4.5 % polyacrylamide gel-17, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMHCV p7 (monomer)-1[U-100% 13C; U-100% 15N; U-80% 2H]1
200 mMDPC-21
25 mMMES-31
0.8 mMHCV p7 (monomer)-4[U-100% 13C; U-100% 15N]2
200 mMDPC-5[U-2H]2
25 mMMES-62
0.8 mMHCV p7 (monomer)-7[U-15% 13C]3
200 mMDPC-8[U-2H]3
25 mMMES-93
0.4 mMHCV p7 (monomer)-10[U-15N; U-2H]4
0.4 mMHCV p7 (monomer)-11[U-13C]4
200 mMDPC-12[U-2H]4
25 mMMES-134
0.2 mMHCV p7 (monomer)-14[U-100% 13C; U-100% 15N; U-80% 2H]5
100 mMDPC-155
25 mMMES-165
4.5 %polyacrylamide gel-175
Sample conditionsIonic strength: 50 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
XEASYBartels et al.data analysis
XEASYBartels et al.noe assignment
TALOSCornilescu, Delaglio and Baxchemical shift calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 1488 / NOE long range total count: 144 / Protein phi angle constraints total count: 234 / Protein psi angle constraints total count: 234
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 60 / Conformers submitted total number: 15 / Representative conformer: 1

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