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- PDB-4adp: HCV-J6 NS5B POLYMERASE V405I MUTANT -

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Basic information

Entry
Database: PDB / ID: 4adp
TitleHCV-J6 NS5B POLYMERASE V405I MUTANT
ComponentsRNA-DIRECTED RNA POLYMERASE
KeywordsTRANSFERASE / HEPACIVIRUS / NONSTRUCTURAL PROTEINS / REPLICATION / RNA-DIRECTED RNA POLYMERASE / RDRP / DE NOVO INITIATION / PRIMING
Function / homology
Function and homology information


hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / 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 / viral process / ribonucleoside triphosphate phosphatase activity ...hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / 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 / viral process / ribonucleoside triphosphate phosphatase activity / lipid droplet / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / 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 / ribonucleoprotein complex / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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 / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / 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 / 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. / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal 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
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHEPATITIS C VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.902 Å
AuthorsScrima, N. / Bressanelli, S.
CitationJournal: J.Virol. / Year: 2012
Title: Two Crucial Early Steps in RNA Synthesis by the Hepatitis C Virus Polymerase Involve a Dual Role of Residue 405.
Authors: Scrima, N. / Caillet-Saguy, C. / Ventura, M. / Harrus, D. / Astier-Gin, T. / Bressanelli, S.
History
DepositionJan 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-DIRECTED RNA POLYMERASE


Theoretical massNumber of molelcules
Total (without water)64,5791
Polymers64,5791
Non-polymers00
Water10,665592
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.500, 95.600, 114.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RNA-DIRECTED RNA POLYMERASE / RNA DEPENDENT RNA POLYMERASE


Mass: 64579.090 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 2443-3012 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HEPATITIS C VIRUS / Strain: J6 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9QF35, UniProt: P26660*PLUS, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 592 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, VAL 2847 TO ILE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 6.5 / Details: 2.17% PEG 4000, 0.05 M TRI-SODIUM CITRATE, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.9→44 Å / Num. obs: 56181 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 13.2
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 2 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXREFINEphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2XWH

2xwh


Resolution: 1.902→44.105 Å / SU ML: 0.43 / σ(F): 1.99 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2009 2845 5.1 %
Rwork0.1713 --
obs0.1729 56168 99.72 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.9 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.6358 Å20 Å20 Å2
2--9.848 Å20 Å2
3----8.2122 Å2
Refinement stepCycle: LAST / Resolution: 1.902→44.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4398 0 0 592 4990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064499
X-RAY DIFFRACTIONf_angle_d1.0086109
X-RAY DIFFRACTIONf_dihedral_angle_d11.2121672
X-RAY DIFFRACTIONf_chiral_restr0.066689
X-RAY DIFFRACTIONf_plane_restr0.005777
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9017-1.93450.35731520.30142566X-RAY DIFFRACTION97
1.9345-1.96970.26691490.23232607X-RAY DIFFRACTION100
1.9697-2.00750.22021340.21542660X-RAY DIFFRACTION100
2.0075-2.04850.28941300.20862626X-RAY DIFFRACTION100
2.0485-2.09310.261530.22422616X-RAY DIFFRACTION100
2.0931-2.14180.25551180.18722684X-RAY DIFFRACTION100
2.1418-2.19530.20681640.18322604X-RAY DIFFRACTION100
2.1953-2.25470.2331230.19432665X-RAY DIFFRACTION100
2.2547-2.3210.25241370.18282660X-RAY DIFFRACTION100
2.321-2.39590.21171280.16842667X-RAY DIFFRACTION100
2.3959-2.48150.20851410.17322642X-RAY DIFFRACTION100
2.4815-2.58090.20321280.17032678X-RAY DIFFRACTION100
2.5809-2.69830.21531650.16842640X-RAY DIFFRACTION100
2.6983-2.84060.20981490.16342647X-RAY DIFFRACTION100
2.8406-3.01850.18761310.16552695X-RAY DIFFRACTION100
3.0185-3.25150.1871440.16352677X-RAY DIFFRACTION100
3.2515-3.57860.1821280.15932716X-RAY DIFFRACTION100
3.5786-4.09610.16731550.1442700X-RAY DIFFRACTION100
4.0961-5.15940.15581400.13622740X-RAY DIFFRACTION100
5.1594-44.11660.18451760.17612833X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 53.6256 Å / Origin y: 61.1633 Å / Origin z: 21.4253 Å
111213212223313233
T0.1243 Å2-0.015 Å2-0.0117 Å2-0.1375 Å20.0294 Å2--0.1736 Å2
L0.4533 °2-0.0718 °20.1125 °2-0.884 °2-0.9385 °2--2.046 °2
S-0.003 Å °-0.07 Å °-0.0353 Å °0.0722 Å °-0.1239 Å °-0.0956 Å °0.0657 Å °0.1207 Å °0.0592 Å °
Refinement TLS groupSelection details: CHAIN A AND (RESSEQ 1:563)

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