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- PDB-4ry5: C-terminal mutant (W550N) of HCV/J4 RNA polymerase -

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Basic information

Entry
Database: PDB / ID: 4ry5
TitleC-terminal mutant (W550N) 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 / : ...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
: / URIDINE 5'-TRIPHOSPHATE / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus isolate HC-J4
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.71 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,9578
Polymers126,7692
Non-polymers1,1886
Water7,638424
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A: HCV J4 RNA polymerase (NS5B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9794
Polymers63,3851
Non-polymers5943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HCV J4 RNA polymerase (NS5B)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9794
Polymers63,3851
Non-polymers5943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.490, 107.946, 133.250
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: 63384.633 Da / Num. of mol.: 2 / Fragment: UNP residues 2420-2989 / Mutation: W550N
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: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.99 Å3/Da / Density % sol: 58.89 %
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: 2.71→21.88 Å / Num. all: 40622 / Num. obs: 42052 / % possible obs: 96.6 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 1 / Redundancy: 5.3 % / Rsym value: 0.138 / Net I/σ(I): 12.2
Reflection shellResolution: 2.71→2.76 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.7 / % possible all: 94

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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: 2.71→19.98 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 2704 6.67 %RANDOM
Rwork0.1656 ---
obs0.1711 40562 96.9 %-
all-40622 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8784 0 62 424 9270
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099094
X-RAY DIFFRACTIONf_angle_d1.2712366
X-RAY DIFFRACTIONf_dihedral_angle_d16.6513500
X-RAY DIFFRACTIONf_chiral_restr0.0461380
X-RAY DIFFRACTIONf_plane_restr0.0181570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.75930.31711390.221914X-RAY DIFFRACTION94
2.7593-2.81220.28381150.22221913X-RAY DIFFRACTION94
2.8122-2.86950.34511330.21311934X-RAY DIFFRACTION95
2.8695-2.93170.30581450.21391938X-RAY DIFFRACTION95
2.9317-2.99970.31331230.20061934X-RAY DIFFRACTION95
2.9997-3.07440.29491350.19981963X-RAY DIFFRACTION96
3.0744-3.15720.31531350.18721968X-RAY DIFFRACTION96
3.1572-3.24970.27851420.18611947X-RAY DIFFRACTION96
3.2497-3.35420.27761390.1791984X-RAY DIFFRACTION97
3.3542-3.47340.28781540.17181978X-RAY DIFFRACTION97
3.4734-3.61170.25081550.15671979X-RAY DIFFRACTION98
3.6117-3.77510.21481470.15522024X-RAY DIFFRACTION98
3.7751-3.97260.21341520.13932004X-RAY DIFFRACTION98
3.9726-4.21930.20921350.13472037X-RAY DIFFRACTION98
4.2193-4.54160.21081170.12112051X-RAY DIFFRACTION98
4.5416-4.99220.21591490.12592050X-RAY DIFFRACTION99
4.9922-5.69980.21731730.1542022X-RAY DIFFRACTION98
5.6998-7.12660.22771490.17192074X-RAY DIFFRACTION98
7.1266-19.98080.19931670.15922144X-RAY DIFFRACTION98
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)
10.38780.15260.28190.7280.15640.68820.10940.0495-0.22110.0318-0.0093-0.1240.35940.0486-0.02680.23110.0164-0.03640.1303-0.0190.224225.614258.091955.3785
20.07280.0028-0.01060.3689-0.30590.69390.0098-0.0268-0.0070.0788-0.0404-0.0679-0.00280.05060.01810.0965-0.0117-0.0240.13740.00090.126525.11247.124926.5963
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A)
2X-RAY DIFFRACTION2(chain B)

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