[English] 日本語
Yorodumi
- PDB-5eqs: Crystal structure of a genotype 1a/3a chimeric HCV NS3/4A proteas... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eqs
TitleCrystal structure of a genotype 1a/3a chimeric HCV NS3/4A protease in complex with Asunaprevir
ComponentsNS3 protease
KeywordsHYDROLASE/HYDROLASE Inhibitor / Asunaprevir / drug resistance / HCV protease inhibitor / Genotype 3 / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


symbiont-mediated transformation of host cell / host cell membrane / serine-type peptidase activity / host cell / symbiont entry into host cell / virion attachment to host cell / virion membrane / proteolysis / metal ion binding / membrane
Similarity search - Function
Thrombin, subunit H - #120 / Hepatitis C virus, NS3 protease, Peptidase S29 / Hepatitis C virus NS3 protease / Hepacivirus/Pegivirus NS3 protease domain profile. / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-2R9 / NS3 protease / NS3 protease
Similarity search - Component
Biological speciesHepatitis C virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.839 Å
AuthorsSoumana, D. / Yilmaz, N.K. / Ali, A. / Prachanronarong, K.L. / Schiffer, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI085051 United States
Citation
Journal: J.Am.Chem.Soc. / Year: 2016
Title: Molecular and Dynamic Mechanism Underlying Drug Resistance in Genotype 3 Hepatitis C NS3/4A Protease.
Authors: Soumana, D.I. / Kurt Yilmaz, N. / Ali, A. / Prachanronarong, K.L. / Schiffer, C.A.
#1: Journal: ACS Chem. Biol. / Year: 2014
Title: Structural analysis of asunaprevir resistance in HCV NS3/4A protease.
Authors: Soumana, D.I. / Ali, A. / Schiffer, C.A.
History
DepositionNov 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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: NS3 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1173
Polymers20,3031
Non-polymers8142
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.115, 60.334, 79.646
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein NS3 protease


Mass: 20302.951 Da / Num. of mol.: 1 / Mutation: D168Q, I132L, R123T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis C virus / Plasmid: pET28-a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: C1KIK8, UniProt: A0A0B4WYC6*PLUS
#2: Chemical ChemComp-2R9 / N-(tert-butoxycarbonyl)-3-methyl-L-valyl-(4R)-4-[(7-chloro-4-methoxyisoquinolin-1-yl)oxy]-N-{(1R,2S)-1-[(cyclopropylsulfonyl)carbamoyl]-2-ethenylcyclopropyl}-L-prolinamide / Asunaprevir


Mass: 748.286 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H46ClN5O9S
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 to 26% PEG-3350, 0.1 M sodium MES buffer at pH 6.5, and 4% ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.839→26.549 Å / Num. all: 15651 / Num. obs: 15651 / % possible obs: 92 % / Redundancy: 4.4 % / Biso Wilson estimate: 13.41 Å2 / Rpim(I) all: 0.047 / Rrim(I) all: 0.106 / Rsym value: 0.094 / Net I/av σ(I): 6.493 / Net I/σ(I): 10.2 / Num. measured all: 69630
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.839-1.892.10.4461.815247240.3670.446259.1
1.89-1.942.40.3652.120208510.2710.3652.672
1.94-1.992.80.2822.726849750.1870.2823.583.8
1.99-2.063.40.2423.2347910300.1430.2424.489.6
2.06-2.124.40.2373.344279960.1190.2375.593
2.12-2.24.60.1953.9471910290.0970.1956.495.3
2.2-2.284.60.1654.6463910060.0830.1657.497.2
2.28-2.374.60.1544.945339810.0780.1547.798.7
2.37-2.484.70.1435.245169570.0710.1438.499.4
2.48-2.64.90.1345.545029190.0660.1349.499.7
2.6-2.7450.1176.343628740.0580.11710.499.8
2.74-2.915.20.0927.542748240.0440.09213.299.9
2.91-3.115.20.0848.541087830.040.08414.599.9
3.11-3.365.40.0768.640067480.0360.07616.7100
3.36-3.685.50.0651037036720.030.06519.8100
3.68-4.115.50.0659.534466270.030.06520.999.9
4.11-4.755.40.0649.530335580.0290.06423.4100
4.75-5.825.40.05910.325724800.0280.05920100
5.82-8.225.20.0639.220053870.030.06318.5100
8.22-26.5494.70.0579.910782300.0280.05720.797

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.28 Å25.33 Å
Translation2.28 Å25.33 Å

-
Processing

Software
NameVersionClassification
SCALA3.3.20data scaling
PHASER2.5.5phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3m5n

3m5n


Resolution: 1.839→25.328 Å / FOM work R set: 0.8356 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2446 1537 10.02 %Random
Rwork0.1927 13802 --
obs0.1979 15339 90.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.4 Å2 / Biso mean: 16.26 Å2 / Biso min: 4.08 Å2
Refinement stepCycle: final / Resolution: 1.839→25.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1371 0 98 33 1502
Biso mean--11.85 18.42 -
Num. residues----192
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151444
X-RAY DIFFRACTIONf_angle_d1.6211984
X-RAY DIFFRACTIONf_chiral_restr0.398240
X-RAY DIFFRACTIONf_plane_restr0.008251
X-RAY DIFFRACTIONf_dihedral_angle_d13.744552
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.839-1.89870.2973850.250975283755
1.8987-1.96650.28441070.2139971107872
1.9665-2.04520.26051310.20021167129885
2.0452-2.13820.26961380.19221245138392
2.1382-2.25090.23311420.19211294143695
2.2509-2.39180.22921490.18921338148797
2.3918-2.57630.23911530.19971365151898
2.5763-2.83530.29111530.20791370152399
2.8353-3.24480.25921550.20381391154699
3.2448-4.08540.23691560.175914061562100
4.0854-25.330.20211680.176915031671100

+
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