[English] 日本語
Yorodumi
- PDB-5gsw: Crystal structure of EV71 3C in complex with N69S 1.8k -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5gsw
TitleCrystal structure of EV71 3C in complex with N69S 1.8k
Components3C protein
KeywordsHYDROLASE / Protease
Function / homology
Function and homology information


T=pseudo3 icosahedral viral capsid / host cell cytoplasm / cysteine-type endopeptidase activity / proteolysis / cytoplasm
Similarity search - Function
Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-5GI / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsWang, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China81330036 China
CitationJournal: Antimicrob. Agents Chemother. / Year: 2017
Title: Structure of the Enterovirus 71 3C Protease in Complex with NK-1.8k and Indications for the Development of Antienterovirus Protease Inhibitor
Authors: Wang, Y. / Cao, L. / Zhai, Y. / Yin, Z. / Sun, Y. / Shang, L.
History
DepositionAug 17, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Nov 8, 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
Revision 1.3Mar 20, 2024Group: Source and taxonomy / Category: entity_src_gen

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3C protein
B: 3C protein
C: 3C protein
D: 3C protein
E: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,03310
Polymers100,8115
Non-polymers2,2225
Water55831
1
A: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6072
Polymers20,1621
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6072
Polymers20,1621
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6072
Polymers20,1621
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6072
Polymers20,1621
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: 3C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6072
Polymers20,1621
Non-polymers4441
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.501, 70.535, 94.923
Angle α, β, γ (deg.)90.00, 118.23, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
3C protein


Mass: 20162.107 Da / Num. of mol.: 5 / Mutation: N69S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: E7E815
#2: Chemical
ChemComp-5GI / ~{N}-[(2~{S})-3-(4-fluorophenyl)-1-oxidanylidene-1-[[(2~{S})-1-oxidanylidene-3-[(3~{S})-2-oxidanylidenepiperidin-3-yl]propan-2-yl]amino]propan-2-yl]-5-methyl-1,2-oxazole-3-carboxamide


Mass: 444.456 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C22H25FN4O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: 0.1 M Tris-HCl, pH 7.7, 200 mM Sodium Citrate, 16% PEG 3350.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 17983 / % possible obs: 96.8 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 7.36
Reflection shellResolution: 3.2→8.67 Å / Rmerge(I) obs: 0.581

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OSY

3osy


Resolution: 3.19→48.62 Å / SU ML: 0.48 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 26.93
RfactorNum. reflection% reflection
Rfree0.268 1831 10.18 %
Rwork0.189 --
obs0.197 17983 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.19→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6981 0 160 31 7172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127286
X-RAY DIFFRACTIONf_angle_d1.6229864
X-RAY DIFFRACTIONf_dihedral_angle_d18.4542639
X-RAY DIFFRACTIONf_chiral_restr0.0591135
X-RAY DIFFRACTIONf_plane_restr0.0061263
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1901-3.27630.37981220.33481072X-RAY DIFFRACTION84
3.2763-3.37270.3781240.26561218X-RAY DIFFRACTION94
3.3727-3.48150.30431420.23571189X-RAY DIFFRACTION95
3.4815-3.60590.32221300.22291219X-RAY DIFFRACTION95
3.6059-3.75020.32971510.2051209X-RAY DIFFRACTION96
3.7502-3.92080.25431390.18571241X-RAY DIFFRACTION97
3.9208-4.12750.27931370.16631262X-RAY DIFFRACTION98
4.1275-4.38590.22421340.15291280X-RAY DIFFRACTION99
4.3859-4.72430.25081440.13981279X-RAY DIFFRACTION100
4.7243-5.19920.20731540.15481267X-RAY DIFFRACTION100
5.1992-5.95040.25831580.18511288X-RAY DIFFRACTION100
5.9504-7.49240.26311350.19791303X-RAY DIFFRACTION100
7.4924-48.62260.21941610.17131325X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6350.3668-0.16030.81460.11691.5339-0.0380.08940.0016-0.1351-0.05830.0240.23750.0353-00.2140.007-0.00460.05770.01740.099610.4428-1.218921.1246
21.56581.0251.08072.26140.7670.7586-0.0272-0.02840.01330.0134-0.01250.0783-0.0705-0.025300.10640.01390.01860.0969-0.00570.110618.300730.943933.7138
31.4938-0.3971-0.61651.1452-0.02681.55670.0383-0.0999-0.1847-0.120.0813-0.0482-0.04330.29100.1314-0.03570.00790.21080.00490.1804-22.135336.033915.7013
41.88090.1546-0.16591.32350.84020.97260.09590.29470.0043-0.206-0.0165-0.0564-0.0053-0.212300.1528-0.0008-0.01380.18740.06620.131639.043433.37795.5627
51.09820.6272-0.01271.59970.10590.7311-0.12630.01020.2309-0.14930.12720.02920.1324-0.3864-00.1801-0.0337-0.02310.3391-0.00370.2381-22.2358-1.698732.3772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E

+
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://pdbjlvh1.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