[English] 日本語
Yorodumi
- PDB-4gh4: Crystal Structure of Foot and Mouth Disease Virus A22 Serotype -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gh4
TitleCrystal Structure of Foot and Mouth Disease Virus A22 Serotype
Components
  • capsid protein VP1
  • capsid protein VP2
  • capsid protein VP3
  • capsid protein VP4
KeywordsVIRUS / icosahedral virus / capsids / picornavirus / apthovirus
Function / homology
Function and homology information


icosahedral viral capsid / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / viral capsid / protein complex oligomerization / monoatomic ion channel activity / regulation of translation ...icosahedral viral capsid / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / viral capsid / protein complex oligomerization / monoatomic ion channel activity / regulation of translation / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / RNA helicase activity / viral protein processing / symbiont entry into host cell / 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 / cytoplasm
Similarity search - Function
Foot-And-Mouth Disease Virus, subunit 4 / Capsid protein VP4 superfamily, Picornavirus / 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 ...Foot-And-Mouth Disease Virus, subunit 4 / Capsid protein VP4 superfamily, Picornavirus / 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 / Jelly Rolls - #20 / 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 / Few Secondary Structures / Irregular / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / 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 / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus - type A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKotecha, A. / Jinshan, R. / Curry, S. / Fry, E. / Stuart, D.
CitationJournal: Structure / Year: 1996
Title: Perturbations in the surface structure of A22 Iraq foot-and-mouth disease virus accompanying coupled changes in host cell specificity and antigenicity.
Authors: Curry, S. / Fry, E. / Blakemore, W. / Abu-Ghazaleh, R. / Jackson, T. / King, A. / Lea, S. / Newman, J. / Rowlands, D. / Stuart, D.
History
DepositionAug 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: capsid protein VP1
B: capsid protein VP2
C: capsid protein VP3
D: capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)75,5114
Polymers75,5114
Non-polymers00
Water4,648258
1
A: capsid protein VP1
B: capsid protein VP2
C: capsid protein VP3
D: capsid protein VP4
x 60


Theoretical massNumber of molelcules
Total (without water)4,530,659240
Polymers4,530,659240
Non-polymers00
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: capsid protein VP1
B: capsid protein VP2
C: capsid protein VP3
D: capsid protein VP4
x 5


  • icosahedral pentamer
  • 378 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)377,55520
Polymers377,55520
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: capsid protein VP1
B: capsid protein VP2
C: capsid protein VP3
D: capsid protein VP4
x 6


  • icosahedral 23 hexamer
  • 453 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)453,06624
Polymers453,06624
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: capsid protein VP1
B: capsid protein VP2
C: capsid protein VP3
D: capsid protein VP4
x 15


  • crystal asymmetric unit, crystal frame
  • 1.13 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,132,66560
Polymers1,132,66560
Non-polymers00
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)328.200, 341.800, 363.750
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain AAAA,CCCC, using strict)
NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.809, 0.309), (0.809, 0.309, -0.5), (0.309, 0.5, 0.809)
3generate(-0.309, -0.5, 0.809), (0.5, -0.809, -0.309), (0.809, 0.309, 0.5)
4generate(-0.309, 0.5, 0.809), (-0.5, -0.809, 0.309), (0.809, -0.309, 0.5)
5generate(0.5, 0.809, 0.309), (-0.809, 0.309, 0.5), (0.309, -0.5, 0.809)
6generate(1), (1), (1)
7generate(0.309, 0.5, 0.809), (0.5, -0.809, 0.309), (0.809, 0.309, -0.5)
8generate(0.809, 0.309, 0.5), (-0.309, -0.5, 0.809), (0.5, -0.809, -0.309)
9generate(0.809, -0.309, 0.5), (-0.309, 0.5, 0.809), (-0.5, -0.809, 0.309)
10generate(0.309, -0.5, 0.809), (0.5, 0.809, 0.309), (-0.809, 0.309, 0.5)
11generate(1), (1), (1)
12generate(0.809, 0.309, -0.5), (0.309, 0.5, 0.809), (0.5, -0.809, 0.309)
13generate(0.5, -0.809, -0.309), (0.809, 0.309, 0.5), (-0.309, -0.5, 0.809)
14generate(-0.5, -0.809, 0.309), (0.809, -0.309, 0.5), (-0.309, 0.5, 0.809)
15generate(-0.809, 0.309, 0.5), (0.309, -0.5, 0.809), (0.5, 0.809, 0.309)

-
Components

#1: Protein capsid protein VP1


Mass: 22962.051 Da / Num. of mol.: 1 / Fragment: UNP residues 440-649 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type A / Strain: FMDV A22 Iraq / References: UniProt: Q9Q2N8, UniProt: Q6PN23*PLUS
#2: Protein capsid protein VP2


Mass: 23347.385 Da / Num. of mol.: 1 / Fragment: UNP residues 12-218 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type A / Strain: FMDV A22 Iraq / References: UniProt: Q9Q2N8, UniProt: Q6PN23*PLUS
#3: Protein capsid protein VP3


Mass: 24245.127 Da / Num. of mol.: 1 / Fragment: UNP residues 219-439 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type A / Strain: FMDV A22 Iraq / References: UniProt: Q9Q2N8
#4: Protein/peptide capsid protein VP4


Mass: 4956.417 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Foot-and-mouth disease virus - type A / Strain: FMDV A22 Iraq / References: UniProt: Q9ILY1*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 22

-
Sample preparation

CrystalDensity Matthews: 4.5 Å3/Da / Density % sol: 72.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 3.8-4.5% PEG20000, 2.5 M ammonium chloride, 4% 1,4-dioxane, 0.1 M sodium phosphate, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12941
21
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONSRS PX9.61
SYNCHROTRONSRS PX9.52
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 483707 / Num. obs: 251190 / % possible obs: 61.7 % / Rmerge(I) obs: 0.179

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.11data extraction
MOSFLMdata reduction
ROTAVATAdata scaling
Agrovatadata scaling
X-PLORphasing
X-PLORrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→25 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: NONE / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: STRUCTURE WAS REFINED WITHOUT FREE R CROSS-VALIDATION
RfactorNum. reflection% reflection
Rwork0.1667 --
Rfree-0 0 %
all-483707 -
obs-251190 61.7 %
Solvent computationBsol: 35.6411 Å2
Displacement parametersBiso max: 120.13 Å2 / Biso mean: 19.4541 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--1.108 Å20 Å20 Å2
2---0.39 Å20 Å2
3---1.498 Å2
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5199 0 0 258 5457
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it8.6888
X-RAY DIFFRACTIONc_scbond_it12.53412
X-RAY DIFFRACTIONc_mcangle_it10.65416
X-RAY DIFFRACTIONc_scangle_it14.58820
X-RAY DIFFRACTIONc_angle_deg1.652
X-RAY DIFFRACTIONc_bond_d0.01
Refine LS restraints NCSRms: 0 / Type: strict / Weight: 300
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_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://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