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- PDB-5qj1: CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS GENOTYPE 2A STRAIN JFH... -

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Basic information

Entry
Database: PDB / ID: 5qj1
TitleCRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS GENOTYPE 2A STRAIN JFH1 L30S NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 6-(ethylamino)-2-(4-fluorophenyl)-5-(3-{[1-(5-fluoropyrimidin-2-yl)cyclopropyl]carbamoyl}-4-methoxyphenyl)-N-methyl-1-benzofuran-3-carboxamide
ComponentsRNA-dependent RNA polymerase
KeywordsTRANSFERASE/TRANSFERASE inhibitor / RDRP STRUCTURE (FINGERS / PALM / THUMB DOMAINS) / ACETYLATION / APOPTOSIS / ATP-BINDING / CAPSID PROTEIN / CELL MEMBRANE / CYTOPLASM / DISULFIDE BOND / ENDOPLASMIC RETICULUM / ENVELOPE PROTEIN / FUSION PROTEIN / GLYCOPROTEIN / HELICASE / HOST-VIRUS INTERACTION / HYDROLASE / INTERFERON ANTIVIRAL SYSTEM EVASION / LIPID DROPLET / LIPOPROTEIN / MEMBRANE / METAL- BINDING / MITOCHONDRION / MULTIFUNCTIONAL ENZYME / NUCLEOTIDE- BINDING / NUCLEOTIDYLTRANSFERASE / NUCLEUS / ONCOGENE / PALMITATE / PHOSPHOPROTEIN / PROTEASE / RIBONUCLEOPROTEIN / RNA REPLICATION / RNA-BINDING / RNA-DIRECTED RNA POLYMERASE / SECRETED / SERINE PROTEASE / SH3-BINDING / THIOL PROTEASE / TRANSCRIPTION / TRANSCRIPTION REGULATION / TRANSFERASE / TRANSMEMBRANE / UBL CONJUGATION / VIRAL NUCLEOPROTEIN / VIRION / ZINC / TRANSFERASE-TRANSFERASE inhibitor complex
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 / Dectin-2 family / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell mitochondrion / 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 ...hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / Dectin-2 family / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell mitochondrion / 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 / lipid droplet / ribonucleoside triphosphate phosphatase 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 / symbiont entry into host cell / 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 / identical protein binding / membrane / plasma membrane / cytoplasm
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
Chem-J6J / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHepacivirus C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.17 Å
AuthorsSheriff, S.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Structure-Property Basis for Solving Transporter-Mediated Efflux and Pan-Genotypic Inhibition in HCV NS5B Inhibitors.
Authors: Yeung, K.S. / Beno, B.R. / Mosure, K. / Zhu, J. / Grant-Young, K.A. / Parcella, K. / Anjanappa, P. / Bora, R.O. / Selvakumar, K. / Wang, Y.K. / Fang, H. / Krause, R. / Rigat, K. / Liu, M. / ...Authors: Yeung, K.S. / Beno, B.R. / Mosure, K. / Zhu, J. / Grant-Young, K.A. / Parcella, K. / Anjanappa, P. / Bora, R.O. / Selvakumar, K. / Wang, Y.K. / Fang, H. / Krause, R. / Rigat, K. / Liu, M. / Lemm, J. / Sheriff, S. / Witmer, M. / Tredup, J. / Jardel, A. / Kish, K. / Parker, D. / Haskell, R. / Santone, K. / Meanwell, N.A. / Soars, M.G. / Roberts, S.B. / Kadow, J.F.
History
DepositionAug 13, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 12, 2021Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNA-dependent RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,44519
Polymers63,9311
Non-polymers2,51318
Water5,801322
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.440, 116.550, 64.710
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-602-

SO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein RNA-dependent RNA polymerase


Mass: 63931.406 Da / Num. of mol.: 1
Fragment: N-TERMINAL CATALYTIC REGION, UNP RESIDUES 2443- 3007
Mutation: L30S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepacivirus C / Strain: 1 / Plasmid: PET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: R9THT8, UniProt: Q99IB8*PLUS, RNA-directed RNA polymerase

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Non-polymers , 5 types, 340 molecules

#2: Chemical ChemComp-J6J / 6-(ethylamino)-2-(4-fluorophenyl)-5-(3-{[1-(5-fluoropyrimidin-2-yl)cyclopropyl]carbamoyl}-4-methoxyphenyl)-N-methyl-1-benzofuran-3-carboxamide


Mass: 597.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H29F2N5O4
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / 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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM sodium citrate, pH 4.6, 200 mM (NH4)2SO4, 25% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.17→46.72 Å / Num. obs: 38057 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 30.22 Å2 / Rsym value: 0.114 / Net I/σ(I): 13.1
Reflection shellResolution: 2.17→2.29 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.544 / Rejects: 0 / % possible all: 99.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALAdata scaling
AMoREphasing
BUSTER2.11.7refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YUY

1yuy


Resolution: 2.17→21.32 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.201 / SU Rfree Blow DPI: 0.163 / SU Rfree Cruickshank DPI: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1898 5 %RANDOM
Rwork0.177 ---
obs0.179 37962 99.7 %-
Displacement parametersBiso max: 125.47 Å2 / Biso mean: 29.74 Å2 / Biso min: 10.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.9187 Å20 Å20 Å2
2---4.593 Å20 Å2
3---1.6743 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: final / Resolution: 2.17→21.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 185 322 4710
Biso mean--41.85 39.31 -
Num. residues----543
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1522SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes775HARMONIC5
X-RAY DIFFRACTIONt_it4478HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion578SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5342SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4478HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6102HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion3.36
X-RAY DIFFRACTIONt_other_torsion16.98
LS refinement shellResolution: 2.17→2.23 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.2203 151 5.16 %
Rwork0.1875 2777 -
all0.1893 2928 -
obs--99.29 %

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