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- PDB-1fmd: THE STRUCTURE AND ANTIGENICITY OF A TYPE C FOOT-AND-MOUTH DISEASE... -

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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 / IRES-dependent viral translational initiation / symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral capsid / regulation of translation / host cell ...L-peptidase / IRES-dependent viral translational initiation / symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral capsid / regulation of translation / host cell / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / symbiont entry into host cell / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
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 / Papain-like cysteine peptidase superfamily / 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 / Picornavirus/Calicivirus coat protein / Few Secondary Structures / Irregular / Viral coat protein subunit / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)

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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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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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

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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

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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

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