[English] 日本語
Yorodumi
- PDB-2xwh: HCV-J6 NS5B polymerase structure at 1.8 Angstrom -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xwh
TitleHCV-J6 NS5B polymerase structure at 1.8 Angstrom
ComponentsRNA DEPENDENT RNA POLYMERASE
KeywordsTRANSFERASE / REPLICATION
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 / viral process / 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 ...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 / viral process / 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 / 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 / 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 / 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 / helicase superfamily c-terminal 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
DI(HYDROXYETHYL)ETHER / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesHEPATITIS C VIRUS ISOLATE HC-J6
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsScrima, N. / Bressanelli, S.
CitationJournal: J.Virol. / Year: 2011
Title: A Comprehensive Structure-Function Comparison of Hepatitis C Virus Strains Jfh1 and J6 Polymerases Reveals a Key Residue Stimulating Replication in Cell Culture Across Genotypes.
Authors: Schmitt, M. / Scrima, N. / Radujkovic, D. / Caillet-Saguy, C. / Simister, P.C. / Friebe, P. / Wicht, O. / Klein, R. / Bartenschlager, R. / Lohmann, V. / Bressanelli, S.
History
DepositionNov 3, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2011Provider: 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 / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA DEPENDENT RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0598
Polymers62,6211
Non-polymers6,4387
Water15,583865
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.830, 94.300, 113.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein RNA DEPENDENT RNA POLYMERASE / GENOME POLYPROTEIN


Mass: 62620.824 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 2443-3005
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HEPATITIS C VIRUS ISOLATE HC-J6 / Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9QF35, UniProt: P26660*PLUS, RNA-directed RNA polymerase
#2: Chemical
ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 865 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.57 % / Description: NONE
Crystal growpH: 8 / Details: 0.1M TRIS PH8 10% PEG 300

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC CCD / Detector: CCD / Date: May 23, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→48.56 Å / Num. obs: 64666 / % possible obs: 99.4 % / Observed criterion σ(I): -4 / Redundancy: 3 % / Biso Wilson estimate: 16.14 Å2 / Rsym value: 0.11 / Net I/σ(I): 7.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.56 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3I5K

3i5k


Resolution: 1.8→42.66 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 18.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2047 3267 5.1 %
Rwork0.164 --
obs0.1661 64666 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.837 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 18.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.2655 Å20 Å20 Å2
2--0.1101 Å20 Å2
3----0.3756 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4375 0 65 865 5305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064541
X-RAY DIFFRACTIONf_angle_d1.016138
X-RAY DIFFRACTIONf_dihedral_angle_d14.2761685
X-RAY DIFFRACTIONf_chiral_restr0.064687
X-RAY DIFFRACTIONf_plane_restr0.005774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.86430.2693050.2366103X-RAY DIFFRACTION100
1.8643-1.9390.25413500.20486060X-RAY DIFFRACTION100
1.939-2.02720.21623180.17566097X-RAY DIFFRACTION100
2.0272-2.13410.22383110.16446117X-RAY DIFFRACTION100
2.1341-2.26780.19513320.14876109X-RAY DIFFRACTION100
2.2678-2.44290.20963130.15156153X-RAY DIFFRACTION100
2.4429-2.68870.21163350.15196153X-RAY DIFFRACTION100
2.6887-3.07760.18823190.15516197X-RAY DIFFRACTION100
3.0776-3.87710.18183260.14826215X-RAY DIFFRACTION99
3.8771-42.67240.17643580.14816195X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 54.0083 Å / Origin y: 60.44 Å / Origin z: 21.3974 Å
111213212223313233
T0.0041 Å2-0.0005 Å20.0018 Å2-0.008 Å20.0123 Å2--0.0155 Å2
L0.1536 °2-0.0663 °20.1123 °2-0.3564 °2-0.4282 °2--0.7799 °2
S0.0024 Å °-0.005 Å °-0.0006 Å °0.0142 Å °-0.0324 Å °-0.016 Å °0.0368 Å °0.0312 Å °0.0247 Å °
Refinement TLS groupSelection details: CHAIN A AND (RESSEQ 1:563)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more