[English] 日本語
Yorodumi
- PDB-5hxf: Crystal structure of 3C protease from a mild Human enterovirus 71... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hxf
TitleCrystal structure of 3C protease from a mild Human enterovirus 71 in complex with rupintrivir
Components3C protease
KeywordsHYDROLASE / enterovirus
Function / homology
Function and homology information


RNA-protein covalent cross-linking / : / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...RNA-protein covalent cross-linking / : / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / ribonucleoside triphosphate phosphatase activity / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / host cell cytoplasm / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain ...Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Trypsin-like serine proteases / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Chem-AG7 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesEnterovirus A71
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsLi, B. / Yuan, Z. / Qin, L. / Gu, L.
CitationJournal: To Be Published
Title: Crystal structure of 3C protease from a mild Human enterovirus 71 in complex with rupintrivir
Authors: Li, B. / Yue, Y. / Zhang, Y. / Yuan, Z. / Liu, Y. / Li, P. / Song, N. / Li, Z. / Gu, L. / Qin, L.
History
DepositionJan 30, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3C protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0864
Polymers20,2931
Non-polymers7933
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-25 kcal/mol
Surface area8430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.209, 64.781, 38.323
Angle α, β, γ (deg.)90.00, 113.06, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein 3C protease


Mass: 20293.260 Da / Num. of mol.: 1 / Fragment: UNP residues 1549-1731
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterovirus A71 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0M3PZC0, UniProt: B8YLW0*PLUS
#2: Chemical ChemComp-AG7 / 4-{2-(4-FLUORO-BENZYL)-6-METHYL-5-[(5-METHYL-ISOXAZOLE-3-CARBONYL)-AMINO]-4-OXO-HEPTANOYLAMINO}-5-(2-OXO-PYRROLIDIN-3-YL)-PENTANOIC ACID ETHYL ESTER / RUPINTRIVIR, bound form


Mass: 600.678 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H41FN4O7 / Comment: antivirus, protease inhibitor*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.04 Å3/Da / Density % sol: 39.64 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 4.5 / Details: 28% PEG 8000, Acetate PH4.5, 0.2M Li2SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. obs: 32549 / % possible obs: 99 % / Redundancy: 3.7 % / Net I/σ(I): 22.38

-
Processing

Software
NameVersionClassification
PHENIX(dev_2257: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OSY

3osy


Resolution: 1.39→23.224 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.14
RfactorNum. reflection% reflection
Rfree0.1991 2017 6.2 %
Rwork0.1743 --
obs0.1758 32549 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.39→23.224 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1405 0 53 236 1694
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081563
X-RAY DIFFRACTIONf_angle_d1.1912130
X-RAY DIFFRACTIONf_dihedral_angle_d14.254573
X-RAY DIFFRACTIONf_chiral_restr0.087242
X-RAY DIFFRACTIONf_plane_restr0.005276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.39-1.42470.26731460.22652136X-RAY DIFFRACTION98
1.4247-1.46330.25511410.22362151X-RAY DIFFRACTION99
1.4633-1.50630.24881490.20782181X-RAY DIFFRACTION99
1.5063-1.55490.2431420.20472165X-RAY DIFFRACTION99
1.5549-1.61050.21591380.20022174X-RAY DIFFRACTION99
1.6105-1.67490.23731460.19782186X-RAY DIFFRACTION100
1.6749-1.75110.23341420.18672178X-RAY DIFFRACTION100
1.7511-1.84340.24671370.19012195X-RAY DIFFRACTION100
1.8434-1.95890.21611490.18422187X-RAY DIFFRACTION100
1.9589-2.110.18421470.16632185X-RAY DIFFRACTION100
2.11-2.32220.19011440.16422195X-RAY DIFFRACTION100
2.3222-2.65780.21851440.17992186X-RAY DIFFRACTION100
2.6578-3.34690.19571470.1672217X-RAY DIFFRACTION100
3.3469-23.22720.15291450.15152196X-RAY DIFFRACTION98

+
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