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- PDB-4ry4: C-terminal mutant (Y448F) of HCV/J4 RNA polymerase -

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Basic information

Entry
Database: PDB / ID: 4ry4
TitleC-terminal mutant (Y448F) of HCV/J4 RNA polymerase
ComponentsHCV J4 RNA polymerase (NS5B)
KeywordsTRANSFERASE / Hepatitis C virus / replication / function analysis / viral RNA polymerase / 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 / : ...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 / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / molecular adaptor activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / ribonucleoprotein complex / 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 / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / 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 / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHepatitis C virus isolate HC-J4
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.59 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 1.2Sep 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)126,8812
Polymers126,8812
Non-polymers00
Water6,305350
1
A: HCV J4 RNA polymerase (NS5B)


Theoretical massNumber of molelcules
Total (without water)63,4411
Polymers63,4411
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)63,4411
Polymers63,4411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.594, 108.352, 134.249
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: 63440.742 Da / Num. of mol.: 2 / Fragment: UNP residues 2420-2989 / Mutation: Y448F
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 / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 3.03 Å3/Da / Density % sol: 59.36 %
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: 2.59→30 Å / Num. all: 48596 / Num. obs: 43746 / % possible obs: 90 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 1 / Redundancy: 2.87 % / Rsym value: 0.067 / Net I/σ(I): 18.7
Reflection shellResolution: 2.59→2.63 Å / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 3.65 / % possible all: 91.4

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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: 2.59→19.9 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 2717 6.47 %RANDOM
Rwork0.1768 ---
obs0.1815 43746 86.54 %-
all-48596 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8769 0 0 350 9119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098961
X-RAY DIFFRACTIONf_angle_d1.34812163
X-RAY DIFFRACTIONf_dihedral_angle_d15.5473315
X-RAY DIFFRACTIONf_chiral_restr0.0491377
X-RAY DIFFRACTIONf_plane_restr0.0071553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.6360.35041380.23281898X-RAY DIFFRACTION81
2.636-2.68660.28891210.22061988X-RAY DIFFRACTION84
2.6866-2.74130.30531210.20752006X-RAY DIFFRACTION84
2.7413-2.80070.27671530.20591990X-RAY DIFFRACTION84
2.8007-2.86570.27031440.20582002X-RAY DIFFRACTION85
2.8657-2.93710.27871330.19662041X-RAY DIFFRACTION86
2.9371-3.01630.30741540.20662059X-RAY DIFFRACTION88
3.0163-3.10470.29561320.21242079X-RAY DIFFRACTION88
3.1047-3.20450.31081520.20192099X-RAY DIFFRACTION89
3.2045-3.31860.29281560.20152079X-RAY DIFFRACTION88
3.3186-3.45080.2781450.18592107X-RAY DIFFRACTION89
3.4508-3.6070.23941480.16652118X-RAY DIFFRACTION89
3.607-3.79590.21331400.16512146X-RAY DIFFRACTION90
3.7959-4.03190.20231510.14942105X-RAY DIFFRACTION89
4.0319-4.34020.20951350.1442125X-RAY DIFFRACTION88
4.3402-4.77160.19561650.13572104X-RAY DIFFRACTION88
4.7716-5.44970.22671450.14932112X-RAY DIFFRACTION87
5.4497-6.82020.23311390.1692123X-RAY DIFFRACTION86
6.8202-19.95090.18421450.14152095X-RAY DIFFRACTION82
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)
10.750.17210.37711.89640.31330.60610.10160.169-0.4270.02090.0198-0.28620.42660.0147-0.09880.3254-0.0169-0.0480.1829-0.06710.309924.900558.357256.0597
20.13150.0425-0.10190.8301-0.8511.58020.0221-0.0719-0.04180.1296-0.1043-0.1736-0.02770.13940.05960.0964-0.0326-0.04330.1381-0.00220.151425.44197.2126.98
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(Chain A)
2X-RAY DIFFRACTION2(Chain B)

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