[English] 日本語
Yorodumi
- PDB-5twn: CRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS NS5B RNA- DEPENDENT RN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5twn
TitleCRYSTAL STRUCTURE OF THE HEPATITIS C VIRUS 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 / NS5B / POLYMERASE / HCV / FINGERS / PALM / THUMB / TRANSFERASE / TRANSFERASE-TRANSFERASE inhibitor complex
Function / homology
Function and homology information


positive stranded viral RNA replication / 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 / viral genome replication ...positive stranded viral RNA replication / 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 / viral genome replication / 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 / RNA helicase / induction by virus of host autophagy / ribonucleoprotein complex / 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 / 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 / protein-containing complex / 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-23E / Chem-7NG / Genome polyprotein
Similarity search - Component
Biological speciesHepatitis C virus genotype 1b
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 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 / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / computing / entity_src_gen
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 / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NS5B RNA- DEPENDENT RNA POLYMERASE
B: NS5B RNA- DEPENDENT RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,82617
Polymers127,9232
Non-polymers2,90315
Water0
1
A: NS5B RNA- DEPENDENT RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1698
Polymers63,9621
Non-polymers1,2077
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NS5B RNA- DEPENDENT RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6579
Polymers63,9621
Non-polymers1,6968
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.000, 91.100, 233.300
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein NS5B RNA- DEPENDENT RNA POLYMERASE


Mass: 63961.516 Da / Num. of mol.: 2 / Fragment: UNP residues 2420-2992
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus genotype 1b (isolate Con1)
Strain: isolate Con1 / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) STAR / References: UniProt: Q9WMX2, RNA-directed RNA polymerase
#2: Chemical ChemComp-23E / (2E)-3-(4-{[(1-{[(13-cyclohexyl-6-oxo-6,7-dihydro-5H-indolo[1,2-d][1,4]benzodiazepin-10-yl)carbonyl]amino}cyclopentyl)carbonyl]amino}phenyl)prop-2-enoic acid


Mass: 630.732 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C38H38N4O5
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: 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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 200 mM Sodium Potassium Tartrate, 100 mM Sodium Citrate, 1.75 M (NH4)2SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.03→50 Å / Num. obs: 27952 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 76 Å2 / Rsym value: 0.12 / Net I/σ(I): 16.8
Reflection shellResolution: 3.03→3.14 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.589 / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QOZ

3qoz
PDB Unreleased entry


Resolution: 3.04→49.12 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.905 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.369
RfactorNum. reflection% reflectionSelection details
Rfree0.223 1063 3.81 %RANDOM
Rwork0.189 ---
obs0.19 27867 99.9 %-
Displacement parametersBiso max: 177.65 Å2 / Biso mean: 65.72 Å2 / Biso min: 14.44 Å2
Baniso -1Baniso -2Baniso -3
1--14.0621 Å20 Å20 Å2
2--2.5204 Å20 Å2
3---11.5417 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: final / Resolution: 3.04→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8374 0 295 0 8669
Biso mean--71.86 --
Num. residues----1086
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2997SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes158HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1429HARMONIC5
X-RAY DIFFRACTIONt_it8853HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1144SEMIHARMONIC5
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_contact10380SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8853HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg12130HARMONIC21.11
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion18.66
LS refinement shellResolution: 3.04→3.15 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.27 88 3.08 %
Rwork0.214 2768 -
all0.215 2856 -
obs--99.65 %

+
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