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- PDB-2xhw: HCV-J4 NS5B Polymerase Trigonal Crystal Form -

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Basic information

Entry
Database: PDB / ID: 2xhw
TitleHCV-J4 NS5B Polymerase Trigonal Crystal Form
ComponentsRNA-directed RNA polymeraseRNA-dependent RNA polymerase
KeywordsTRANSFERASE / REPLICATION / TRANSCRIPTION
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. / Reverse transcriptase/Diguanylate cyclase domain / 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. / Alpha-Beta Plaits / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHepatitis C virus genotype 1b
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsHarrus, D. / Ahmed-El-Sayed, N. / Simister, P.C. / Miller, S. / Triconnet, M. / Hagedorn, C.H. / Mahias, K. / Rey, F.A. / Astier-Gin, T. / Bressanelli, S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Further Insights Into the Roles of GTP and the C- Terminus of the Hepatitis C Virus Polymerase in the Initiation of RNA Synthesis
Authors: Harrus, D. / Ahmed-El-Sayed, N. / Simister, P.C. / Miller, S. / Triconnet, M. / Hagedorn, C.H. / Mahias, K. / Rey, F.A. / Astier-Gin, T. / Bressanelli, S.
History
DepositionJun 21, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _citation.page_last / _database_2.pdbx_DOI ..._citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Mar 27, 2024Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)64,5991
Polymers64,5991
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.400, 125.400, 140.080
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein RNA-directed RNA polymerase / RNA-dependent RNA polymerase / NS5B / p68


Mass: 64598.988 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 2420-2989
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus genotype 1b (strain HC-J4)
Strain: HC-J4 / Plasmid: PET23A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O92972, RNA-directed RNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 4.93 Å3/Da / Density % sol: 75.06 % / Description: NONE
Crystal growpH: 7 / Details: 2-6% PEG 3350, 0.2 M NAF, PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Type: SLS / Wavelength: 1.0079
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0079 Å / Relative weight: 1
ReflectionResolution: 2.6→19.7 Å / Num. obs: 36792 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 9.1 % / Biso Wilson estimate: 41.01 Å2 / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.59
Reflection shellResolution: 2.66→2.72 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2.55 / % possible all: 92.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.6_289)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NB4

1nb4


Resolution: 2.66→19.7 Å / SU ML: 0.28 / σ(F): 1.39 / Phase error: 20.37 / Stereochemistry target values: ML / Details: RESIDUES 564-569 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.221 1831 5 %
Rwork0.17 --
obs0.172 36792 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.84 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 44.58 Å2
Baniso -1Baniso -2Baniso -3
1--2.7032 Å20 Å20 Å2
2---2.7032 Å20 Å2
3---5.4064 Å2
Refinement stepCycle: LAST / Resolution: 2.66→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4366 0 0 139 4505
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084461
X-RAY DIFFRACTIONf_angle_d1.1166055
X-RAY DIFFRACTIONf_dihedral_angle_d17.6411632
X-RAY DIFFRACTIONf_chiral_restr0.074686
X-RAY DIFFRACTIONf_plane_restr0.004772
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.656-2.75070.32031460.24463188X-RAY DIFFRACTION91
2.7507-2.86050.32991730.2133515X-RAY DIFFRACTION100
2.8605-2.99020.22881780.19823472X-RAY DIFFRACTION100
2.9902-3.14730.24561740.19443498X-RAY DIFFRACTION100
3.1473-3.34360.24961810.20323501X-RAY DIFFRACTION100
3.3436-3.60030.24511840.18313506X-RAY DIFFRACTION100
3.6003-3.95990.24142130.17313478X-RAY DIFFRACTION100
3.9599-4.52690.19531810.14293560X-RAY DIFFRACTION100
4.5269-5.68060.16451970.12793553X-RAY DIFFRACTION100
5.6806-19.69580.17642040.1423690X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -41.7603 Å / Origin y: 34.376 Å / Origin z: -2.72 Å
111213212223313233
T0.108 Å2-0.0857 Å20.0004 Å2-0.0683 Å20.0017 Å2--0.0242 Å2
L0.9531 °20.4845 °2-0.6884 °2-0.7491 °2-0.5203 °2--0.9229 °2
S0.0466 Å °-0.0278 Å °0.0057 Å °0.0982 Å °-0.0642 Å °0.0501 Å °0.0451 Å °0.0995 Å °0.0211 Å °
Refinement TLS groupSelection details: CHAIN A

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