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- PDB-4ry6: C-terminal mutant (W550A) of HCV/J4 RNA polymerase -

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Basic information

Entry
Database: PDB / ID: 4ry6
TitleC-terminal mutant (W550A) of HCV/J4 RNA polymerase
ComponentsHCV J4 RNA polymerase (NS5B)
KeywordsTRANSFERASE / Hepatitis C virus / replication / function analysis / viral RNA polymerase / RdRp / RNA RNTP MG / nucleotide transfer
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 / molecular adaptor activity / 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-J4
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.52 Å
AuthorsJaeger, J. / Cherry, A. / Dennis, C.
CitationJournal: J.Virol. / Year: 2015
Title: Hydrophobic and Charged Residues in the C-Terminal Arm of Hepatitis C Virus RNA-Dependent RNA Polymerase Regulate Initiation and Elongation.
Authors: Cherry, A.L. / Dennis, C.A. / Baron, A. / Eisele, L.E. / Thommes, P.A. / Jaeger, J.
History
DepositionDec 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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: HCV J4 RNA polymerase (NS5B)
B: HCV J4 RNA polymerase (NS5B)


Theoretical massNumber of molelcules
Total (without water)126,6832
Polymers126,6832
Non-polymers00
Water8,089449
1
A: HCV J4 RNA polymerase (NS5B)


Theoretical massNumber of molelcules
Total (without water)63,3421
Polymers63,3421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HCV J4 RNA polymerase (NS5B)


Theoretical massNumber of molelcules
Total (without water)63,3421
Polymers63,3421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)106.153, 107.795, 133.735
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 HCV J4 RNA polymerase (NS5B) / RNA-dependent RNA polymerase


Mass: 63341.609 Da / Num. of mol.: 2 / Fragment: UNP residues 2420-2989 / Mutation: W550A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus isolate HC-J4 / Gene: NS5B / Plasmid: pET23A / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O92972, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 50 mM MES, pH 5.0, 20% PEG4000, 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 11, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.52→49.9 Å / Num. all: 52734 / Num. obs: 49043 / % possible obs: 93 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 1 / Redundancy: 4 % / Rsym value: 0.127 / Net I/σ(I): 19
Reflection shellResolution: 2.52→2.56 Å / Mean I/σ(I) obs: 3.5 / Rsym value: 0.584 / % possible all: 80.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX1.8.4refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1NB4

1nb4


Resolution: 2.52→19.9 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 3391 6.94 %RANDOM
Rwork0.186 ---
obs0.1922 48896 92.98 %-
all-52734 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.52→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8769 0 0 449 9218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098998
X-RAY DIFFRACTIONf_angle_d1.26712219
X-RAY DIFFRACTIONf_dihedral_angle_d14.5733347
X-RAY DIFFRACTIONf_chiral_restr0.0461383
X-RAY DIFFRACTIONf_plane_restr0.0061565
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.52-2.55250.37911150.3051613X-RAY DIFFRACTION81
2.5525-2.59050.37971360.29061729X-RAY DIFFRACTION86
2.5905-2.63090.2991400.26641765X-RAY DIFFRACTION88
2.6309-2.67390.34951210.2621809X-RAY DIFFRACTION89
2.6739-2.71990.38181230.26481770X-RAY DIFFRACTION88
2.7199-2.76920.29671470.23951795X-RAY DIFFRACTION90
2.7692-2.82240.33691420.23761829X-RAY DIFFRACTION92
2.8224-2.87980.35031300.23841862X-RAY DIFFRACTION92
2.8798-2.94220.29821550.21921849X-RAY DIFFRACTION92
2.9422-3.01050.31861440.21641874X-RAY DIFFRACTION92
3.0105-3.08550.29581460.21351886X-RAY DIFFRACTION94
3.0855-3.16860.2821300.19871916X-RAY DIFFRACTION94
3.1686-3.26140.28751410.19021916X-RAY DIFFRACTION95
3.2614-3.36620.28661370.18481942X-RAY DIFFRACTION95
3.3662-3.48590.24421480.18231908X-RAY DIFFRACTION94
3.4859-3.62470.25321380.16631945X-RAY DIFFRACTION96
3.6247-3.78860.26511590.16531949X-RAY DIFFRACTION96
3.7886-3.98690.24261400.14791921X-RAY DIFFRACTION93
3.9869-4.23440.19431420.13821982X-RAY DIFFRACTION97
4.2344-4.55780.21031520.12591999X-RAY DIFFRACTION98
4.5578-5.00990.2181630.13152020X-RAY DIFFRACTION98
5.0099-5.71990.22751340.15782028X-RAY DIFFRACTION97
5.7199-7.15110.23521470.17652049X-RAY DIFFRACTION97
7.1511-19.97470.19911610.15462149X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67670.16930.30041.16060.34360.87990.13940.0778-0.27780.0942-0.0192-0.15020.4850.0259-0.06680.3421-0.0171-0.03570.1757-0.02770.266225.228758.092455.584
20.1860.00630.02230.5672-0.54671.12980.003-0.0418-0.00990.1744-0.0631-0.0801-0.03890.07970.0510.146-0.0338-0.01760.16310.00420.156825.47977.143526.4783
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A )
2X-RAY DIFFRACTION2(chain B )

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