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- PDB-5d8a: Crystal structure of recombinant foot-and-mouth-disease virus A22... -

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Basic information

Entry
Database: PDB / ID: 5d8a
TitleCrystal structure of recombinant foot-and-mouth-disease virus A22-H2093F empty capsid
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / Foot and mouth disease virus / picornavirus / vaccine / aphthovirus
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 / regulation of translation / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / viral protein processing ...symbiont-mediated perturbation of host chromatin organization / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / regulation of translation / 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 - type A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 16, 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

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3
D: VP4


Theoretical massNumber of molelcules
Total (without water)80,7604
Polymers80,7604
Non-polymers00
Water3,531196
1
A: VP1
B: VP2
C: VP3
D: VP4
x 60


Theoretical massNumber of molelcules
Total (without water)4,845,616240
Polymers4,845,616240
Non-polymers00
Water4,324240
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
A: VP1
B: VP2
C: VP3
D: VP4
x 5


  • icosahedral pentamer
  • 404 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)403,80120
Polymers403,80120
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP2
C: VP3
D: VP4
x 6


  • icosahedral 23 hexamer
  • 485 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)484,56224
Polymers484,56224
Non-polymers00
Water43224
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)327.570, 341.290, 363.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Components on special symmetry positions
IDModelComponents
11B-337-

HOH

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)
6generate(1), (1), (1)
7generate(0.309017, 0.5, 0.809017), (0.5, -0.809017, 0.309017), (0.809017, 0.309017, -0.5)
8generate(0.809017, 0.309017, 0.5), (-0.309017, -0.5, 0.809017), (0.5, -0.809017, -0.309017)
9generate(0.809017, -0.309017, 0.5), (-0.309017, 0.5, 0.809017), (-0.5, -0.809017, 0.309017)
10generate(0.309017, -0.5, 0.809017), (0.5, 0.809017, 0.309017), (-0.809017, 0.309017, 0.5)
11generate(1), (1), (1)
12generate(0.809017, 0.309017, -0.5), (0.309017, 0.5, 0.809017), (0.5, -0.809017, 0.309017)
13generate(0.5, -0.809017, -0.309017), (0.809017, 0.309017, 0.5), (-0.309017, -0.5, 0.809017)
14generate(-0.5, -0.809017, 0.309017), (0.809017, -0.309017, 0.5), (-0.309017, 0.5, 0.809017)
15generate(-0.809017, 0.309017, 0.5), (0.309017, -0.5, 0.809017), (0.5, 0.809017, 0.309017)

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Components

#1: Protein VP1


Mass: 23090.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type A / Strain: serotype A22 Iraq / Cell line (production host): BHK-21 Clone 13 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q6PN23
#2: Protein VP2


Mass: 24646.828 Da / Num. of mol.: 1 / Mutation: H93F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type A / Strain: serotype A22 Iraq / Cell line (production host): BHK-21, Clone 13 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q6PN23
#3: Protein VP3


Mass: 24245.127 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus - type A / Strain: serotype A22 Iraq / Cell line (production host): BHK-21, Clone 13 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q6PN23
#4: Protein 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 - type A / Strain: serotype A22 Iraq / Cell line (production host): BHK-21, Clone 13 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: Q6PN23
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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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: 4 M ammonium acetate, 100 mM bis-Tris Propane

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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: Jun 24, 2013
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 356924 / % possible obs: 45.7 % / Redundancy: 1.4 % / Rmerge(I) obs: 0.265 / Χ2: 0.907 / Net I/av σ(I): 2.363 / Net I/σ(I): 2.8 / Num. measured all: 498664
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
2.4-2.491.3309560.75839.8
2.49-2.591.4341280.74743.9
2.59-2.71.4365960.754470.937
2.7-2.851.4363380.77746.60.774
2.85-3.021.4364890.80946.90.6
3.02-3.261.4362820.86246.50.374
3.26-3.581.4361780.99146.30.261
3.58-4.11.4363821.01846.60.177
4.1-5.171.4367321.07146.80.134
5.17-501.4368431.20846.30.126

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Processing

Software
NameVersionClassification
CNSrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IV1

4iv1


Resolution: 2.4→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 17454 2.2 %Random selection
Rwork0.206 330470 --
obs-347924 44.5 %-
Solvent computationBsol: 40.9934 Å2
Displacement parametersBiso max: 158.33 Å2 / Biso mean: 28.8024 Å2 / Biso min: 3.83 Å2
Baniso -1Baniso -2Baniso -3
1--3.98 Å20 Å20 Å2
2--1.022 Å20 Å2
3---2.957 Å2
Refinement stepCycle: final / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5188 0 0 196 5384
Biso mean---31.96 -
Num. residues----663
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it6.838
X-RAY DIFFRACTIONc_scbond_it11.36812
X-RAY DIFFRACTIONc_mcangle_it8.84916
X-RAY DIFFRACTIONc_scangle_it12.74120
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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