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

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Basic information

Entry
Database: PDB / ID: 5twm
TitleCRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS GENOTYPE 2A STRAIN JFH1 L30S NS5B RNA-DEPENDENT RNA POLYMERASE IN COMPLEX WITH 5-[3-(tert-butylcarbamoyl)phenyl]-6-(ethylamino)-2-(4-fluorophenyl)-N-methylfuro[2,3-b]pyridine-3-carboxamide
ComponentsNS5B RNA-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


negative regulation of autophagy of mitochondrion / : / 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 / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity ...negative regulation of autophagy of mitochondrion / : / 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 / 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 / negative regulation of autophagy / 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 / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / ribonucleoprotein complex / induction by virus of host autophagy / 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 / 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 / identical protein binding
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
Chem-7NG / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus genotype 2a
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSheriff, S.
CitationJournal: Medchemcomm / Year: 2017
Title: The discovery of a pan-genotypic, primer grip inhibitor of HCV NS5B polymerase.
Authors: Eastman, K.J. / Parcella, K. / Yeung, K.S. / Grant-Young, K.A. / Zhu, J. / Wang, T. / Zhang, Z. / Yin, Z. / Beno, B.R. / Sheriff, S. / Kish, K. / Tredup, J. / Jardel, A.G. / Halan, V. / ...Authors: Eastman, K.J. / Parcella, K. / Yeung, K.S. / Grant-Young, K.A. / Zhu, J. / Wang, T. / Zhang, Z. / Yin, Z. / Beno, B.R. / Sheriff, S. / Kish, K. / Tredup, J. / Jardel, A.G. / Halan, V. / Ghosh, K. / Parker, D. / Mosure, K. / Fang, H. / Wang, Y.K. / Lemm, J. / Zhuo, X. / Hanumegowda, U. / Rigat, K. / Donoso, M. / Tuttle, M. / Zvyaga, T. / Haarhoff, Z. / Meanwell, N.A. / Soars, M.G. / Roberts, S.B. / Kadow, J.F.
History
DepositionNov 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2Oct 31, 2018Group: Data collection / Database references / Category: citation / citation_author / computing
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _computing.structure_solution
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NS5B RNA-dependent RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5919
Polymers63,9311
Non-polymers1,6608
Water6,900383
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.687, 89.816, 216.745
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-602-

SO4

21A-1026-

HOH

31A-1035-

HOH

41A-1048-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NS5B RNA-dependent RNA POLYMERASE


Mass: 63931.406 Da / Num. of mol.: 1 / Fragment: UNP residues 2443-3015 / Mutation: L30S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus genotype 2a (isolate JFH-1)
Strain: isolate JFH-1 / Gene: NS5B / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q99IB8, RNA-directed RNA polymerase

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Non-polymers , 5 types, 391 molecules

#2: Chemical ChemComp-7NG / 5-[3-(tert-butylcarbamoyl)phenyl]-6-(ethylamino)-2-(4-fluorophenyl)-N-methylfuro[2,3-b]pyridine-3-carboxamide


Mass: 488.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H29FN4O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.46 Å3/Da / Density % sol: 50.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM Sodium Acetate, 25% (W/V) PEG 4000, 200 mM (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / 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 wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→44.91 Å / Num. obs: 44742 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 25.95 Å2 / Rsym value: 0.069 / Net I/σ(I): 19.5
Reflection shellResolution: 1.97→2.08 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.465 / Rejects: 0 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YUY

1yuy


Resolution: 1.97→42.47 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.909 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.153 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.134
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2257 5.05 %RANDOM
Rwork0.169 ---
obs0.171 44687 99.1 %-
Displacement parametersBiso max: 117.75 Å2 / Biso mean: 29.66 Å2 / Biso min: 11.71 Å2
Baniso -1Baniso -2Baniso -3
1-6.126 Å20 Å20 Å2
2---11.632 Å20 Å2
3---5.5059 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: final / Resolution: 1.97→42.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4322 0 109 383 4814
Biso mean--45.61 38.23 -
Num. residues----559
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1561SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes700HARMONIC5
X-RAY DIFFRACTIONt_it4555HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion590SEMIHARMONIC5
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_contact5670SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4555HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg6197HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion16.3
LS refinement shellResolution: 1.97→2.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 149 5.01 %
Rwork0.186 2828 -
all0.188 2977 -
obs--90.3 %

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