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- PDB-3gsz: Structure of the genotype 2B HCV polymerase -

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Basic information

Entry
Database: PDB / ID: 3gsz
TitleStructure of the genotype 2B HCV polymerase
ComponentsRNA-directed RNA polymerase
KeywordsTRANSFERASE / polymerase / HCV
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 / SH3 domain binding / nucleoside-triphosphate phosphatase ...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 / SH3 domain binding / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / 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 / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / ribonucleoprotein complex / 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 / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / ATP hydrolysis 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, 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 NS2, C-terminal domain / 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, 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 NS2, C-terminal domain / 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 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 zinc finger domain / Hepatitis C virus non-structural 5a domain 1b / Hepatitis C virus, Non-structural protein NS2 / : / NS3 RNA helicase, C-terminal helical domain / Hepacivirus nonstructural protein 2 (NS2) protease domain profile. / Hepatitis C virus non-structural 5a protein membrane anchor / 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 / Hepacivirus/Pegivirus NS3 protease domain profile. / Hepatitis C virus NS3 protease / 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 isolate HC-J8
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRydberg, E.H. / Carfi, A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural basis for resistance of the genotype 2b hepatitis C virus NS5B polymerase to site A non-nucleoside inhibitors.
Authors: Rydberg, E.H. / Cellucci, A. / Bartholomew, L. / Mattu, M. / Barbato, G. / Ludmerer, S.W. / Graham, D.J. / Altamura, S. / Paonessa, G. / De Francesco, R. / Migliaccio, G. / Carfi, A.
History
DepositionMar 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: RNA-directed RNA polymerase
B: RNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)125,5402
Polymers125,5402
Non-polymers00
Water14,862825
1
A: RNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)62,7701
Polymers62,7701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)62,7701
Polymers62,7701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)153.251, 64.497, 135.583
Angle α, β, γ (deg.)90.00, 90.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein RNA-directed RNA polymerase / NS5B


Mass: 62769.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus isolate HC-J8 / Production host: Escherichia coli (E. coli) / References: UniProt: P26661
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 825 / Source method: isolated from a natural source / Formula: H2O

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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: 2.67 Å3/Da / Density % sol: 53.91 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 6.5mg/ml enzyme, 10% PEG4K, 100mM NaCitrate, 200mM NaCl, 5mM DTT , pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 6, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 104470 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rsym value: 0.073
Reflection shellResolution: 1.9→1.949 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3 / Num. unique all: 9159 / Rsym value: 0.366 / % possible all: 87

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NS5B genotype 2a

Resolution: 1.9→19.96 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 2.976 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21006 5127 5 %RANDOM
Rwork0.16646 ---
obs0.16868 96413 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.996 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20.4 Å2
2--0.22 Å20 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8746 0 0 825 9571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0218942
X-RAY DIFFRACTIONr_bond_other_d0.0020.028218
X-RAY DIFFRACTIONr_angle_refined_deg1.871.95412134
X-RAY DIFFRACTIONr_angle_other_deg0.976319046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63851112
X-RAY DIFFRACTIONr_chiral_restr0.1360.21362
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029896
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021886
X-RAY DIFFRACTIONr_nbd_refined0.220.21804
X-RAY DIFFRACTIONr_nbd_other0.250.29333
X-RAY DIFFRACTIONr_nbtor_other0.0890.25374
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2546
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.228
X-RAY DIFFRACTIONr_mcbond_it1.3441.55578
X-RAY DIFFRACTIONr_mcangle_it2.44629018
X-RAY DIFFRACTIONr_scbond_it3.78733364
X-RAY DIFFRACTIONr_scangle_it6.1084.53116
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 327
Rwork0.197 6168

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