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- PDB-2wzr: The Structure of Foot and Mouth Disease Virus Serotype SAT1 -

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Basic information

Entry
Database: PDB / ID: 2wzr
TitleThe Structure of Foot and Mouth Disease Virus Serotype SAT1
Components(POLYPROTEIN) x 4
KeywordsVIRUS / CAPSID / RNA REPLICATION / RNA-DIRECTED RNA POLYMERASE / NUCLEOTIDYLTRANSFERASE / HOST CYTOPLASMIC VESICLE / CAPSID PROTEIN
Function / homology
Function and homology information


symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane ...symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / 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
Biological speciesFOOT-AND-MOUTH DISEASE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 3 Å
AuthorsAdams, P. / Lea, S. / Newman, J. / Blakemore, W. / King, A. / Stuart, D. / Fry, E.
Citation
Journal: To be Published
Title: The Structure of Foot-and-Mouth Disease Virus Serotype Sat1.
Authors: Adams, P. / Lea, S. / Newman, J. / Blakemore, W. / King, A. / Stuart, D. / Fry, E.
#1: Journal: To be Published
Title: Using Capsid Sequence Data to Predict Cross Reactivity and Select Vaccines for Foot-and-Mouth Disease
Authors: Reeve, R. / Blignaut, B. / Esterhuysen, J.J. / Opperman, P. / Matthews, L. / Fry, E. / De Beer, T.A.P. / Theron, J. / Rieder, E. / Vosloo, W. / O'Neill, H.G. / Haydon, D.T. / Maree, F.F.
History
DepositionDec 2, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: POLYPROTEIN
2: POLYPROTEIN
3: POLYPROTEIN
4: POLYPROTEIN


Theoretical massNumber of molelcules
Total (without water)81,9084
Polymers81,9084
Non-polymers00
Water00
1
1: POLYPROTEIN
2: POLYPROTEIN
3: POLYPROTEIN
4: POLYPROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)4,914,479240
Polymers4,914,479240
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: POLYPROTEIN
2: POLYPROTEIN
3: POLYPROTEIN
4: POLYPROTEIN
x 5


  • icosahedral pentamer
  • 410 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)409,54020
Polymers409,54020
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: POLYPROTEIN
2: POLYPROTEIN
3: POLYPROTEIN
4: POLYPROTEIN
x 6


  • icosahedral 23 hexamer
  • 491 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)491,44824
Polymers491,44824
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: POLYPROTEIN
2: POLYPROTEIN
3: POLYPROTEIN
4: POLYPROTEIN
x 60


  • crystal asymmetric unit, crystal frame
  • 4.91 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)4,914,479240
Polymers4,914,479240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)305.140, 305.140, 723.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.494194, -0.642336, 0.585813), (0.86918, 0.378489, -0.318235), (-0.01731, 0.666446, 0.745352)-0.01126, 0.00603, 0.00493
3generate(-0.324218, -0.170142, 0.930556), (0.764026, -0.627138, 0.151532), (0.557805, 0.760098, 0.333323)-0.0178, -0.00304, 0.01281
4generate(-0.324218, 0.764026, 0.557805), (-0.170142, -0.627138, 0.760098), (0.930556, 0.151532, 0.333323)-0.01059, -0.01468, 0.01276
5generate(0.494194, 0.86918, -0.01731), (-0.642336, 0.378489, 0.666446), (0.585813, -0.318235, 0.745352)0.00041, -0.0128, 0.00484
6generate(-0.803371, -0.106812, 0.585822), (-0.106812, -0.941978, -0.318227), (0.585822, -0.318227, 0.745349)-0.01078, 0.0067, 0.00484
7generate(-0.5, 0.866025, 1.0E-5), (-0.866025, -0.5, 7.0E-6), (1.1E-5, -5.0E-6, 1)0.00051, 0.00065
8generate(0.505635, 0.648955, -0.568499), (-0.862574, 0.36704, -0.348207), (-0.017309, 0.666438, 0.74536)0.01136, 0.00739, 0.00493
9generate(0.82378, -0.458039, -0.334044), (-0.101228, 0.460922, -0.881649), (0.557798, 0.760099, 0.333332)0.00677, 0.01759, 0.01281
10generate(0.014771, -0.925129, 0.379365), (0.365859, -0.348096, -0.86312), (0.930553, 0.151543, 0.333325)-0.00691, 0.01717, 0.01276
11generate(-0.544286, 0.8389, -4.0E-6), (0.8389, 0.544286, -7.0E-6), (-4.0E-6, -7.0E-6, -1)0.00053, -0.00029, 0.03959
12generate(0.460172, 0.667126, -0.58582), (0.887661, -0.332854, 0.318223), (0.017302, -0.666447, -0.745352)0.01172, -0.00645, 0.03466
13generate(0.817407, -0.433503, -0.37937), (0.143858, -0.48408, 0.863117), (-0.557809, -0.760093, -0.333327)0.00767, -0.01688, 0.02678
14generate(0.033732, -0.941955, 0.334039), (-0.364599, 0.299598, 0.881651), (-0.930553, -0.15153, -0.33333)-0.00601, -0.01716, 0.02683
15generate(-0.80784, -0.155567, 0.568501), (0.06496, 0.935163, 0.348211), (-0.585811, 0.318229, -0.745356)-0.01042, -0.00691, 0.03475
16generate(0.347657, -0.732088, -0.585818), (-0.732088, -0.602308, 0.318234), (-0.585818, 0.318234, -0.745349)0.01202, -0.00569, 0.03475
17generate(-0.454365, -0.890815, -3.0E-6), (-0.890815, 0.454365, 5.0E-6), (-3.0E-6, 5.0E-6, -1)0.00081, 0.00049, 0.03959
18generate(-0.998823, -0.04531, 0.017313), (-0.04531, 0.744178, -0.666443), (0.017313, -0.666443, -0.745355)0.00055, 0.01326, 0.03466
19generate(-0.533294, 0.635969, -0.5578), (0.635969, -0.133381, -0.760101), (-0.5578, -0.760101, -0.333325)0.01161, 0.01497, 0.02678
20generate(0.298876, 0.211517, -0.930556), (0.211517, -0.965555, -0.151537), (-0.930556, -0.151537, -0.333321)0.01869, 0.00326, 0.02683

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Components

#1: Protein POLYPROTEIN


Mass: 24161.252 Da / Num. of mol.: 1 / Fragment: RESIDUES 725-943 / Source method: isolated from a natural source / Source: (natural) FOOT-AND-MOUTH DISEASE VIRUS / Strain: SAT1BOT1/68 / References: UniProt: Q6PMU1
#2: Protein POLYPROTEIN


Mass: 24623.590 Da / Num. of mol.: 1 / Fragment: RESIDUES 285-503 / Source method: isolated from a natural source / Source: (natural) FOOT-AND-MOUTH DISEASE VIRUS / Strain: SAT1BOT1/68 / References: UniProt: Q6PMU1
#3: Protein POLYPROTEIN


Mass: 24339.008 Da / Num. of mol.: 1 / Fragment: RESIDUES 504-724 / Source method: isolated from a natural source / Source: (natural) FOOT-AND-MOUTH DISEASE VIRUS / Strain: SAT1BOT1/68 / References: UniProt: Q6PMU1
#4: Protein POLYPROTEIN


Mass: 8784.136 Da / Num. of mol.: 1 / Fragment: RESIDUES 200-284 / Source method: isolated from a natural source / Source: (natural) FOOT-AND-MOUTH DISEASE VIRUS / Strain: SAT1BOT1/68 / References: UniProt: Q6PMU1
Has protein modificationY
Sequence detailsVP1 105 PRO IN STRUCTURE NOT GLN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDescription: NONE

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.875
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.875 Å / Relative weight: 1
ReflectionResolution: 3→17 Å / Num. obs: 300769 / % possible obs: 60 % / Observed criterion σ(I): 0 / Redundancy: 1.6 % / Rmerge(I) obs: 0.23

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 3→17 Å / Cross valid method: NONE / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.23 --
obs0.23 300769 60.1 %
Refinement stepCycle: LAST / Resolution: 3→17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5210 0 0 0 5210
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.99
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

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