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- PDB-5ddj: Crystal structure of recombinant foot-and-mouth-disease virus O1M... -

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Basic information

Entry
Database: PDB / ID: 5ddj
TitleCrystal structure of recombinant foot-and-mouth-disease virus O1M-S2093Y empty capsid
Components
  • Foot and mouth disease virus, VP1Foot-and-mouth disease virus
  • Foot and mouth disease virus, VP2Foot-and-mouth disease virus
  • Foot and mouth disease virus, VP3Foot-and-mouth disease virus
  • Genome polyprotein
KeywordsVIRUS / foot and mouth disease virus / picornavirus / aphthovirus / vaccine
Function / homology
Function and homology information


modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell ...modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / cytoplasmic vesicle membrane / : / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / virion attachment to host cell / proteolysis / RNA binding / ATP binding
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
Biological speciesFoot-and-mouth disease virus - type O
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsKotecha, A. / Seago, J. / Scott, K. / Burman, A. / Loureiro, S. / Ren, J. / Porta, C. / Ginn, H.M. / Jackson, T. / Perez-Martin, E. ...Kotecha, A. / Seago, J. / Scott, K. / Burman, A. / Loureiro, S. / Ren, J. / Porta, C. / Ginn, H.M. / Jackson, T. / Perez-Martin, E. / Siebert, C.A. / Paul, G. / Huiskonen, J.T. / Jones, I.M. / Esnouf, R.M. / Fry, E.E. / Maree, F.F. / Charleston, B. / Stuart, D.I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust089755 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2015
Title: Structure-based energetics of protein interfaces guides foot-and-mouth disease virus vaccine design.
Authors: Abhay Kotecha / Julian Seago / Katherine Scott / Alison Burman / Silvia Loureiro / Jingshan Ren / Claudine Porta / Helen M Ginn / Terry Jackson / Eva Perez-Martin / C Alistair Siebert / ...Authors: Abhay Kotecha / Julian Seago / Katherine Scott / Alison Burman / Silvia Loureiro / Jingshan Ren / Claudine Porta / Helen M Ginn / Terry Jackson / Eva Perez-Martin / C Alistair Siebert / Guntram Paul / Juha T Huiskonen / Ian M Jones / Robert M Esnouf / Elizabeth E Fry / Francois F Maree / Bryan Charleston / David I Stuart /
Abstract: Virus capsids are primed for disassembly, yet capsid integrity is key to generating a protective immune response. Foot-and-mouth disease virus (FMDV) capsids comprise identical pentameric protein ...Virus capsids are primed for disassembly, yet capsid integrity is key to generating a protective immune response. Foot-and-mouth disease virus (FMDV) capsids comprise identical pentameric protein subunits held together by tenuous noncovalent interactions and are often unstable. Chemically inactivated or recombinant empty capsids, which could form the basis of future vaccines, are even less stable than live virus. Here we devised a computational method to assess the relative stability of protein-protein interfaces and used it to design improved candidate vaccines for two poorly stable, but globally important, serotypes of FMDV: O and SAT2. We used a restrained molecular dynamics strategy to rank mutations predicted to strengthen the pentamer interfaces and applied the results to produce stabilized capsids. Structural analyses and stability assays confirmed the predictions, and vaccinated animals generated improved neutralizing-antibody responses to stabilized particles compared to parental viruses and wild-type capsids.
History
DepositionAug 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Database references
Revision 1.3Jan 10, 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_initial_refinement_model / pdbx_struct_oper_list
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: Foot and mouth disease virus, VP1
2: Foot and mouth disease virus, VP2
3: Foot and mouth disease virus, VP3
4: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)80,2974
Polymers80,2974
Non-polymers00
Water0
1
1: Foot and mouth disease virus, VP1
2: Foot and mouth disease virus, VP2
3: Foot and mouth disease virus, VP3
4: Genome polyprotein
x 60


Theoretical massNumber of molelcules
Total (without water)4,817,805240
Polymers4,817,805240
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, VP1
2: Foot and mouth disease virus, VP2
3: Foot and mouth disease virus, VP3
4: Genome polyprotein
x 5


  • icosahedral pentamer
  • 401 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)401,48420
Polymers401,48420
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: Foot and mouth disease virus, VP1
2: Foot and mouth disease virus, VP2
3: Foot and mouth disease virus, VP3
4: Genome polyprotein
x 6


  • icosahedral 23 hexamer
  • 482 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)481,78024
Polymers481,78024
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
Unit cell
Length a, b, c (Å)344.080, 344.080, 344.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.809017, 0.309017), (0.809017, 0.309017, -0.5), (0.309017, 0.5, 0.809017)
3generate(-0.309017, -0.5, 0.809017), (0.5, -0.809017, -0.309017), (0.809017, 0.309017, 0.5)
4generate(-0.309017, 0.5, 0.809017), (-0.5, -0.809017, 0.309017), (0.809017, -0.309017, 0.5)
5generate(0.5, 0.809017, 0.309017), (-0.809017, 0.309017, 0.5), (0.309017, -0.5, 0.809017)

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Components

#1: Protein Foot and mouth disease virus, VP1 / Foot-and-mouth disease virus


Mass: 23207.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type O / Cell line (production host): BHK-21, Clone 13 / Production host: MESOCRICETUS AURATUS (golden hamster) / Strain (production host): BHK-21 / References: UniProt: Q6PMW3
#2: Protein Foot and mouth disease virus, VP2 / Foot-and-mouth disease virus


Mass: 24417.510 Da / Num. of mol.: 1 / Mutation: S93Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type O / Cell line (production host): BHK-21, Clone 13 / Production host: MESOCRICETUS AURATUS (golden hamster) / Strain (production host): BHK-21 / References: UniProt: Q6PMW3
#3: Protein Foot and mouth disease virus, VP3 / Foot-and-mouth disease virus


Mass: 23905.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type O / Cell line (production host): BHK-21, Clone 13 / Production host: MESOCRICETUS AURATUS (golden hamster) / Strain (production host): BHK-21 / References: UniProt: Q6PMW3
#4: Protein Genome polyprotein


Mass: 8766.075 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type O / Cell line (production host): BHK-21, Clone 13 / Production host: MESOCRICETUS AURATUS (golden hamster) / Strain (production host): BHK-21 / References: UniProt: Q6PMW3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.5 M ammonium sulphate, 100 mM bis-Tris Propane, pH 7.0
PH range: 7

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionRedundancy: 1.5 % / Number: 67562 / Rmerge(I) obs: 0.427 / Χ2: 0.93 / D res high: 3.5 Å / D res low: 50 Å / Num. obs: 45271 / % possible obs: 53.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
7.535010.141.1421.6
5.987.5310.3540.9531.6
5.235.9810.460.9391.5
4.755.2310.4640.9281.5
4.414.7510.430.9081.5
4.154.4110.4680.9031.5
3.944.1510.60.8831.5
3.773.9410.6950.861.4
3.633.7710.790.7871.5
3.53.6310.9380.8671.4
ReflectionResolution: 3.5→50 Å / Num. obs: 45271 / % possible obs: 53.2 % / Redundancy: 1.5 % / Rmerge(I) obs: 0.427 / Χ2: 0.928 / Net I/av σ(I): 1.547 / Net I/σ(I): 1.7 / Num. measured all: 67562
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.5-3.631.40.93840250.86747.9
3.63-3.771.50.7942970.78750.8
3.77-3.941.40.69542420.8650.1
3.94-4.151.50.643670.88351.6
4.15-4.411.50.46845970.90354.4
4.41-4.751.50.4346100.90854.3
4.75-5.231.50.46445720.92853.7
5.23-5.981.50.4647340.93955.7
5.98-7.531.60.35450070.95358.5
7.53-501.60.1448201.14255.1

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Processing

Software
NameVersionClassification
CNS1.3refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FOD

1fod


Resolution: 3.5→49.664 Å / Cross valid method: NONE / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.361 65914 -
Rfree-0 0 %
obs-65914 77.8 %
Solvent computationBsol: 75.2315 Å2
Displacement parametersBiso max: 135.49 Å2 / Biso mean: 47.2234 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 3.5→49.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 0 0 5132
Num. residues----660
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.81
X-RAY DIFFRACTIONc_mcbond_it6.7054
X-RAY DIFFRACTIONc_scbond_it10.4456
X-RAY DIFFRACTIONc_mcangle_it11.2438
X-RAY DIFFRACTIONc_scangle_it15.57812
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
3.5-3.630.34736118X-RAY DIFFRACTION1072.8
3.63-3.770.35266361X-RAY DIFFRACTION1075.4
3.77-3.940.35586274X-RAY DIFFRACTION1074.8
3.94-4.150.34836433X-RAY DIFFRACTION1076.3
4.15-4.410.35096737X-RAY DIFFRACTION1079.7
4.41-4.750.35796717X-RAY DIFFRACTION1079.5
4.75-5.230.34116654X-RAY DIFFRACTION1078.3
5.23-5.980.35186733X-RAY DIFFRACTION1079.6
5.98-7.530.37927038X-RAY DIFFRACTION1082.5
7.53-49.660.40056849X-RAY DIFFRACTION1078.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.paramCNS_TOPPAR:carbohydrate.top

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