[English] 日本語
Yorodumi
- PDB-2bhg: 3C protease from type A10(61) foot-and-mouth disease virus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bhg
Title3C protease from type A10(61) foot-and-mouth disease virus
ComponentsFOOT-AND-MOUTH DISEASE VIRUS 3C PROTEASE
KeywordsHYDROLASE / FOOT-AND-MOUTH DISEASE VIRUS / PROTEASE / CHYMOTRYPSIN-LIKE CYSTEINE PROTEASE / CAPSID PROTEIN / CORE PROTEIN / COVALENT PROTEIN-RNA LINKAGE / LIPOPROTEIN / MYRISTATE / POLYPROTEIN / RNA-DIRECTED RNA POLYMERASE / THIOL PROTEASE / TRANSFERASE
Function / homology
Function and homology information


L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization ...L-peptidase / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / 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 / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. ...Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / 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 / Papain-like cysteine peptidase superfamily / 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. / 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
Biological speciesFOOT-AND-MOUTH DISEASE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsBirtley, J.R. / Brick, P. / Curry, S.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of Foot-and-Mouth Disease Virus 3C Protease: New Insights Into Catalytic Mechanism and Cleavage Specificity
Authors: Birtley, J.R. / Knox, S.R. / Jaulent, A.M. / Brick, P. / Leatherbarrow, R.J. / Curry, S.
History
DepositionJan 10, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD BC" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AD BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FOOT-AND-MOUTH DISEASE VIRUS 3C PROTEASE
B: FOOT-AND-MOUTH DISEASE VIRUS 3C PROTEASE


Theoretical massNumber of molelcules
Total (without water)45,9282
Polymers45,9282
Non-polymers00
Water1,76598
1
A: FOOT-AND-MOUTH DISEASE VIRUS 3C PROTEASE


Theoretical massNumber of molelcules
Total (without water)22,9641
Polymers22,9641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: FOOT-AND-MOUTH DISEASE VIRUS 3C PROTEASE


Theoretical massNumber of molelcules
Total (without water)22,9641
Polymers22,9641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)141.589, 141.589, 43.677
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.87858, 0.45631, -0.14099), (0.45779, -0.88875, -0.023683), (-0.14099, -0.043737, -0.98973)
Vector: 0.26814, 4.6677, 10.78)

-
Components

#1: Protein FOOT-AND-MOUTH DISEASE VIRUS 3C PROTEASE


Mass: 22963.785 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS / Strain: A10(61) / Plasmid: PETM-11(3C) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P03306, picornain 3C
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A B, CYS 95 TO LYS ENGINEERED RESIDUE IN CHAIN A B, CYS 142 TO SER ...ENGINEERED RESIDUE IN CHAIN A B, CYS 95 TO LYS ENGINEERED RESIDUE IN CHAIN A B, CYS 142 TO SER ENGINEERED RESIDUE IN CHAIN A B, CYS 163 TO ALA THIS PROTEIN CONTAINS THREE SUBSTITUTED CYS RESIDUES (C95K, C142S) TO ENHANCE SOLUBILITY AND ONE (C163A) WHICH SUBSTITUTES THE ACTIVE SITE NUCLEOPHILE AND THEREFORE INACTIVATES THE ENZYME.
Sequence detailsCRYSTALLISED SEQUENCE CONTAINS AN ADDITIONAL GLY AT N-TERM (RESIDUE NUMBER -1). ALSO CONTAINS ...CRYSTALLISED SEQUENCE CONTAINS AN ADDITIONAL GLY AT N-TERM (RESIDUE NUMBER -1). ALSO CONTAINS TRUNCATED C-TERMINUS (BY 6 RESIDUES). DATABASE ENTRY CONTAINS A PROTEIN SEQUENCE ERROR. THE SEQUENCE 78-RTGHALRRGTHW-89 IN THE DATABASE ENTRY SHOULD BE REPLACED BY 78-GQDMLSDAALMV-89. THIS IS NOT EXPLICITLY CORRECTED IN THE SEQUENCE CONFLICTS GIVEN BELOW (CONFINED TO ENGINEERED MUTATIONS). THE FOLLOWING RESIDUES ARE CONFLICTS BETWEEN THE PROTEIN AND THE UNIPROT ENTRY, BUT SINCE THEY ARE NOT OBSERVED IN THE STRUCTURE, THEY CANNOT BE GIVEN SEQADV RECORDS: B78 (GLY), B79 (GLN), B80 (ASP), B81 (MSE) RESIDUES A142 (SER) AND B142 (SER) ARE ENGINEERED MUTATIONS, BUT THEY ARE NOT OBSERVED AND ARE NOT THEREFORE RECORDED WITH SEQADV RECORDS.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32 %
Crystal growpH: 6.5 / Details: SEE PAPER, pH 6.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 4, 2004 / Details: MIRRORS
RadiationMonochromator: SI 111 - CHANNEL CUT MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→26.8 Å / Num. obs: 25640 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→26.76 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4405866.34 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD F
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1288 5 %RANDOM
Rwork0.218 ---
obs0.218 25721 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.6554 Å2 / ksol: 0.38098 e/Å3
Displacement parametersBiso mean: 35.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.94 Å2-1.29 Å20 Å2
2---5.94 Å20 Å2
3---11.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.9→26.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 0 98 2830
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 209 4.9 %
Rwork0.304 4065 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM

+
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