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- PDB-3mwv: Crystal structure of HCV NS5B polymerase -

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Basic information

Entry
Database: PDB / ID: 3mwv
TitleCrystal structure of HCV NS5B polymerase
ComponentsGenome polyprotein
KeywordsTRANSFERASE / HCV virus RdRp NS5B polymerase
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 / : ...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 / 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 / molecular adaptor activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / RNA helicase / induction by virus of host autophagy / ribonucleoprotein complex / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
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 non-structural protein NS4b ...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 / 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
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCoulombe, R.
CitationJournal: J.Am.Chem.Soc. / Year: 2010
Title: Importance of ligand bioactive conformation in the discovery of potent indole-diamide inhibitors of the hepatitis C virus NS5B.
Authors: LaPlante, S.R. / Gillard, J.R. / Jakalian, A. / Aubry, N. / Coulombe, R. / Brochu, C. / Tsantrizos, Y.S. / Poirier, M. / Kukolj, G. / Beaulieu, P.L.
History
DepositionMay 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: Genome polyprotein
B: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)128,5712
Polymers128,5712
Non-polymers00
Water4,594255
1
A: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)64,2861
Polymers64,2861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)64,2861
Polymers64,2861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.270, 108.330, 133.340
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsThere are 2 biological units in the asymmetric unit (chain A & B)

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Components

#1: Protein Genome polyprotein / Core protein p21 / Capsid protein C / p21 / Core protein p19 / Envelope glycoprotein E1 / gp32 / ...Core protein p21 / Capsid protein C / p21 / Core protein p19 / Envelope glycoprotein E1 / gp32 / gp35 / Envelope glycoprotein E2 / NS1 / gp68 / gp70 / p7 / Protease NS2-3 / p23 / Serine protease/NTPase/helicase NS3 / Hepacivirin / NS3P / p70 / Non-structural protein 4A / NS4A / p8 / Non-structural protein 4B / NS4B / p27 / Non-structural protein 5A / NS5A / p56 / RNA-directed RNA polymerase / NS5B / p68


Mass: 64285.637 Da / Num. of mol.: 2 / Fragment: UNP residues 2420 to 2989
Source method: isolated from a genetically manipulated source
Details: delta 21 aa at Cterm + 6His tag / Source: (gene. exp.) Hepatitis C virus / Strain: HC-J4 / Gene: NS5B / Plasmid: PET29b / Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3) / References: UniProt: O92972, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.98 Å3/Da / Density % sol: 58.79 %
Crystal growTemperature: 284 K / Method: vapor diffusion / pH: 5.4
Details: 100mM MES, 21% PEG5Kmme, 400mM AS, 10% glycerol, pH 5.4, vapor diffusion, temperature 284K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Dec 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 76274 / % possible obs: 96.9 % / Redundancy: 6.57 % / Rmerge(I) obs: 0.095 / Χ2: 1.034 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 3.83 / Num. unique all: 6128 / Χ2: 1.079 / % possible all: 78.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.1data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C2P

1c2p


Resolution: 2.2→50 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.835 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.248 7690 9.8 %
Rwork0.219 --
obs-76189 96.8 %
Displacement parametersBiso max: 85.43 Å2 / Biso mean: 30.497 Å2 / Biso min: 8.29 Å2
Baniso -1Baniso -2Baniso -3
1--9.71 Å20 Å20 Å2
2--5.675 Å20 Å2
3---4.034 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8704 0 0 255 8959
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3061.5
X-RAY DIFFRACTIONc_scbond_it2.0952
X-RAY DIFFRACTIONc_mcangle_it2.0352
X-RAY DIFFRACTIONc_scangle_it3.0072.5
X-RAY DIFFRACTIONc_bond_d0.005534
X-RAY DIFFRACTIONc_dihedral_angle_d21.374
X-RAY DIFFRACTIONc_improper_angle_d0.75953
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.210.2921010.25810421143
2.21-2.230.3051220.27910581180
2.23-2.250.3131160.25910961212
2.25-2.260.2441300.23811601290
2.26-2.280.2751360.24311591295
2.28-2.30.2941330.25212131346
2.3-2.310.3121320.25312141346
2.31-2.330.2891210.25812811402
2.33-2.350.2891390.23713221461
2.35-2.370.2721410.24113371478
2.37-2.390.2681490.23313191468
2.39-2.410.2671530.22514211574
2.41-2.430.2371500.22613991549
2.43-2.450.281740.23213921566
2.45-2.480.2651520.22214061558
2.48-2.50.2871360.22714091545
2.5-2.530.2771610.23614111572
2.53-2.550.2781650.21613791544
2.55-2.580.2721540.2414141568
2.58-2.610.2911670.24213841551
2.61-2.640.3121560.24413981554
2.64-2.670.3241450.24814281573
2.67-2.70.2771730.2313891562
2.7-2.740.2731450.24314181563
2.74-2.770.2541650.22514061571
2.77-2.810.2511720.23214061578
2.81-2.850.2481790.22713821561
2.85-2.890.3031470.23814101557
2.89-2.940.2811660.24813971563
2.94-2.990.2481600.23114031563
2.99-3.040.3041570.25414301587
3.04-3.090.2911570.25214061563
3.09-3.150.3011510.24814021553
3.15-3.220.2391520.23314371589
3.22-3.290.2541750.22713891564
3.29-3.360.2491510.23714311582
3.36-3.450.2741910.23813861577
3.45-3.540.251630.22114131576
3.54-3.640.221710.22114031574
3.64-3.760.2141490.21614181567
3.76-3.90.221710.19814361607
3.9-4.050.2011650.18714171582
4.05-4.240.2341450.18214431588
4.24-4.460.1921530.17214471600
4.46-4.740.2081730.16414231596
4.74-5.10.2021610.18214421603
5.1-5.620.2511800.22114431623
5.62-6.430.2371510.24214571608
6.43-8.090.231770.21214821659
8.09-500.1821570.17515411698
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1MSI_CNX_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2MSI_CNX_TOPPAR:water_rep.param

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