[English] 日本語
Yorodumi
- PDB-1fmd: THE STRUCTURE AND ANTIGENICITY OF A TYPE C FOOT-AND-MOUTH DISEASE... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1fmd
TitleTHE STRUCTURE AND ANTIGENICITY OF A TYPE C FOOT-AND-MOUTH DISEASE VIRUS
Components
  • FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP1)
  • FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP2)
  • FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP3)
  • FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP4)
KeywordsVIRUS / Icosahedral virus
Function / homology
Function and homology information


L-peptidase / icosahedral viral capsid / IRES-dependent viral translational initiation / symbiont-mediated perturbation of host chromatin organization / protein complex oligomerization / monoatomic ion channel activity / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane ...L-peptidase / icosahedral viral capsid / IRES-dependent viral translational initiation / symbiont-mediated perturbation of host chromatin organization / protein complex oligomerization / monoatomic ion channel activity / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / viral capsid / regulation of translation / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / RNA helicase activity / host cell endoplasmic reticulum membrane / viral protein processing / induction by virus of host autophagy / symbiont entry into host cell / 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 / membrane / cytoplasm
Similarity search - Function
Foot-And-Mouth Disease Virus, subunit 4 / Capsid protein VP4 superfamily, Picornavirus / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / 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 / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / 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 / Picornavirus coat protein / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / 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 / Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsLea, S. / Fry, E. / Stuart, D.
Citation
Journal: Structure / Year: 1994
Title: The structure and antigenicity of a type C foot-and-mouth disease virus.
Authors: Lea, S. / Hernandez, J. / Blakemore, W. / Brocchi, E. / Curry, S. / Domingo, E. / Fry, E. / Abu-Ghazaleh, R. / King, A. / Newman, J. / Stuart, D. / Mateu, M.G.
#1: Journal: Acta Crystallogr.,Sect.A / Year: 1993
Title: Methods Used in the Structure Determination of Foot and Mouth Disease Virus
Authors: Fry, E. / Acharya, R. / Stuart, D.
#2: Journal: Nature / Year: 1989
Title: The Three-Dimensional Structure of Foot and Mouth Disease Virus at 2.9 Angstroms Resolution
Authors: Acharya, R. / Fry, E. / Stuart, D. / Fox, G. / Rowlands, D. / Brown, F.
History
DepositionFeb 10, 1994Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
1: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP1)
2: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP2)
3: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP3)
4: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP4)


Theoretical massNumber of molelcules
Total (without water)79,7914
Polymers79,7914
Non-polymers00
Water00
1
1: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP1)
2: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP2)
3: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP3)
4: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP4)
x 60


Theoretical massNumber of molelcules
Total (without water)4,787,460240
Polymers4,787,460240
Non-polymers00
Water0
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
1: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP1)
2: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP2)
3: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP3)
4: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP4)
x 5


  • icosahedral pentamer
  • 399 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)398,95520
Polymers398,95520
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP1)
2: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP2)
3: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP3)
4: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP4)
x 6


  • icosahedral 23 hexamer
  • 479 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)478,74624
Polymers478,74624
Non-polymers00
Water0
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
1: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP1)
2: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP2)
3: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP3)
4: FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP4)
x 5


  • crystal asymmetric unit, crystal frame
  • 399 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)398,95520
Polymers398,95520
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)347.600, 347.600, 347.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Atom site foot note1: CIS PROLINE - PRO 1 111 / 2: CIS PROLINE - PRO 2 84
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.80901699, 0.30901699), (0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699)
3generate(-0.30901699, -0.5, 0.80901699), (0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5)
4generate(-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.30901699), (0.80901699, -0.30901699, 0.5)
5generate(0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699)

-
Components

#1: Protein FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP1)


Mass: 22694.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Genus: Aphthovirus / Organ: KIDNEY / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q65095
#2: Protein FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP2)


Mass: 24297.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Genus: Aphthovirus / Organ: KIDNEY / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q9YQQ5, UniProt: P15072*PLUS
#3: Protein FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP3)


Mass: 24020.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Genus: Aphthovirus / Organ: KIDNEY / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q9YQQ5, UniProt: P15072*PLUS
#4: Protein FOOT-AND-MOUTH DISEASE VIRUS (SUBUNIT VP4)


Mass: 8778.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Genus: Aphthovirus / Organ: KIDNEY / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P87677, UniProt: P49303*PLUS
Sequence detailsNOTE: THE SEQUENCE AS PRESENTED IN THE COORDINATES AND THE SEQRES RECORDS BELOW HAS BEEN CONFIRMED ...NOTE: THE SEQUENCE AS PRESENTED IN THE COORDINATES AND THE SEQRES RECORDS BELOW HAS BEEN CONFIRMED BY RESEQUENCING OF THE SPECIFIC VIRUS USED IN THE STRUCTURE DETERMINATION. SWISS-PROT ENTRY POLG_FMDVT PRESENTS THE SEQUENCE OF STRAIN C1. SWISS-PROT ENTRY POLG_FMDVS PRESENTS THE SEQUENCE OF CHAIN 1 AND PART OF CHAIN 3 OF STRAIN C1-SANTA PAU (C-S8). NEITHER OF THESE PRESENTS THE SEQUENCE OF THE STRAIN PRESENTED IN THIS ENTRY.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19.5-11.5 %satammonium sulfate1reservoir
210 mMdithiothreitol1reservoir

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3.5 Å / Num. obs: 64849 / % possible obs: 74 % / Num. measured all: 98942 / Rmerge(I) obs: 0.18

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.5→27 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.204 -
obs0.204 79016
Refinement stepCycle: LAST / Resolution: 3.5→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5169 0 0 0 5169
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.9

+
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