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- PDB-1fod: STRUCTURE OF A MAJOR IMMUNOGENIC SITE ON FOOT-AND-MOUTH DISEASE VIRUS -

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Basic information

Entry
Database: PDB / ID: 1fod
TitleSTRUCTURE OF A MAJOR IMMUNOGENIC SITE ON FOOT-AND-MOUTH DISEASE VIRUS
Components(FOOT AND MOUTH DISEASE VIRUS) x 4
KeywordsVIRUS / Icosahedral virus
Function / homology
Function and homology information


T=pseudo3 icosahedral viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Foot-And-Mouth Disease Virus, subunit 4 / Capsid protein VP4 superfamily, Picornavirus / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Jelly Rolls - #20 / Picornavirus coat protein / Picornavirus capsid / picornavirus capsid protein ...Foot-And-Mouth Disease Virus, subunit 4 / Capsid protein VP4 superfamily, Picornavirus / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Jelly Rolls - #20 / Picornavirus coat protein / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Few Secondary Structures / Irregular / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Genome polyprotein / Genome polyprotein
Similarity search - Component
Biological speciesFoot-and-mouth disease virus
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsLogan, D.T. / Lea, S. / Lewis, R. / Stuart, D. / Fry, E.
Citation
Journal: Nature / Year: 1993
Title: Structure of a major immunogenic site on foot-and-mouth disease virus.
Authors: Logan, D. / Abu-Ghazaleh, R. / Blakemore, W. / Curry, S. / Jackson, T. / King, A. / Lea, S. / Lewis, R. / Newman, J. / Parry, N. / Rowlands, D. / Stuart, D. / Fry, E.
#1: Journal: Semin.Virol. / Year: 1990
Title: Architecture and Topography of an Aphthovirus
Authors: Fry, E. / Logan, D. / Acharya, R. / Fox, G. / Rowlands, D. / Brown, F. / Stuart, D.
#2: Journal: Nature / Year: 1990
Title: Structural and Serological Evidence for a Novel Mechanism of Antigenic Variation in Foot-and-Mouth Disease Virus
Authors: Parry, N. / Fox, G. / Rowlands, D. / Brown, F. / Fry, E. / Acharya, R. / Logan, D. / Stuart, D.
#3: 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
DepositionOct 27, 1993Processing site: BNL
Revision 1.0Jan 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
2: FOOT AND MOUTH DISEASE VIRUS
3: FOOT AND MOUTH DISEASE VIRUS
4: FOOT AND MOUTH DISEASE VIRUS


Theoretical massNumber of molelcules
Total (without water)80,8274
Polymers80,8274
Non-polymers00
Water00
1
1: FOOT AND MOUTH DISEASE VIRUS
2: FOOT AND MOUTH DISEASE VIRUS
3: FOOT AND MOUTH DISEASE VIRUS
4: FOOT AND MOUTH DISEASE VIRUS
x 60


Theoretical massNumber of molelcules
Total (without water)4,849,594240
Polymers4,849,594240
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
2: FOOT AND MOUTH DISEASE VIRUS
3: FOOT AND MOUTH DISEASE VIRUS
4: FOOT AND MOUTH DISEASE VIRUS
x 5


  • icosahedral pentamer
  • 404 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)404,13320
Polymers404,13320
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: FOOT AND MOUTH DISEASE VIRUS
2: FOOT AND MOUTH DISEASE VIRUS
3: FOOT AND MOUTH DISEASE VIRUS
4: FOOT AND MOUTH DISEASE VIRUS
x 6


  • icosahedral 23 hexamer
  • 485 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)484,95924
Polymers484,95924
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
2: FOOT AND MOUTH DISEASE VIRUS
3: FOOT AND MOUTH DISEASE VIRUS
4: FOOT AND MOUTH DISEASE VIRUS
x 5


  • crystal asymmetric unit, crystal frame
  • 404 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)404,13320
Polymers404,13320
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation4
Unit cell
Length a, b, c (Å)345.000, 345.000, 345.000
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


Mass: 23814.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Genus: Aphthovirus / Strain: STRAIN BFS, 1860 / References: UniProt: Q84771
#2: Protein FOOT AND MOUTH DISEASE VIRUS


Mass: 24373.455 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Genus: Aphthovirus / Strain: STRAIN BFS, 1860 / References: UniProt: Q84771
#3: Protein FOOT AND MOUTH DISEASE VIRUS


Mass: 23860.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus / Genus: Aphthovirus / Strain: STRAIN BFS, 1860 / References: UniProt: Q84771
#4: Protein FOOT AND MOUTH DISEASE VIRUS


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 / Strain: STRAIN BFS, 1860 / References: UniProt: P87677
Compound detailsATTACHMENT OF FOOT AND MOUTH DISEASE VIRUS (FMDV) TO ITS CELLULAR RECEPTOR INVOLVES A LONG AND ...ATTACHMENT OF FOOT AND MOUTH DISEASE VIRUS (FMDV) TO ITS CELLULAR RECEPTOR INVOLVES A LONG AND HIGHLY ANTIGENIC LOOP CONTAINING THE CONSERVED ARG-GLY-ASP SEQUENCE, A MOTIF KNOWN TO BE A RECOGNITION ELEMENT IN MANY INTEGRIN-DEPENDENT CELL ADHESION PROCESSES. IN THE ORIGINAL CRYSTAL STRUCTURE OF FMDV (REF 3), THE ARG-GLY-ASP CONTAINING LOOP LOCATED BETWEEN BETA STRANDS G AND H OF CAPSID PROTEIN VP1 WAS DISORDERED. IT WAS SURMISED THAT THE DISORDER WAS ENHANCED BY A DISULFIDE BOND LINKING THE BASE OF THE LOOP CYS 134 TO CYS 130 OF VP2. THESE COORDINATES ARE FOR VIRUS EXPOSED TO A REDUCING ENVIRONMENT (CRYSTALS WERE SOAKED IN 10MM DTT PRIOR TO DATA COLLECTION) SO THAT THE DISULFIDE BRIDGE WAS AT LEAST 85 PER CENT REDUCED. IN THIS STRUCTURE RESIDUES 134 - 157 ADOPT A SINGLE CONFORMATION WHICH IS FOR THE MOST PART UNAMBIGUOUS. HOWEVER, RESIDUES 137 AND 138 OF VP1 WERE DIFFICULT TO MODEL EXACTLY - THEY LIE IN ESSENTIALLY THE CORRECT POSITION BUT THE DEPOSITORS CANNOT BE SURE THAT THE CONFORMATION IS EXACTLY RIGHT. THE REDUCED VIRUS RETAINS INFECTIVITY AND SEROLOGICAL EXPERIMENTS SUGGEST THAT SOME OF THE LOOP'S INTERNAL STRUCTURE IS CONSERVED.
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: POLG_FMDVO SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ILE 780 VAL 1 56 ALA 788 GLY 1 64 ASN 861 SER 1 137 TYR 416 CYS 2 130 GLN 589 HIS 3 85 ALA 672 THR 3 168 GLY 677 ASP 3 173 THE SEQUENCE USED IN THIS ENTRY AGREES WITH THAT DETERMINED BY D. ROWLANDS FOR O1BFS 1860 EXCEPT FOR RESIDUE 173 OF CHAIN 3. THIS DIFFERENCE HAS NOT BEEN RESOLVED BECAUSE THE AUTHORS OF THIS ENTRY FIND THAT THE DENSITY FITS WELL IF THEY ASSUME THAT RESIDUE 173 OF CHAIN 3 IS ASP.

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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-IDChemical formula
317-19 %ammonium sulfate12
40.1 Msodium phosphate12
1ammonium sulfate11
2virus11
512NaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.208 / Rfactor obs: 0.208 / Highest resolution: 2.6 Å
Refinement stepCycle: LAST / Highest resolution: 2.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5363 0 0 0 5363
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.023
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_deg3.7
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
Refinement
*PLUS
Highest resolution: 2.6 Å / Rfactor obs: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.7

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