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- PDB-5ac9: Structure-based energetics of protein interfaces guide Foot-and-M... -

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Basic information

Entry
Database: PDB / ID: 5ac9
TitleStructure-based energetics of protein interfaces guide Foot-and-Mouth disease virus vaccine design
Components
  • VP1
  • VP2
  • VP3
  • VP4
KeywordsVIRUS / VACCINE / FOOT AND MOUTH DISEASE VIRUS / FMDV
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 O
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKotecha, A. / Seago, J. / Scott, K. / Burman, A. / Loureiro, S. / Ren, J. / Porta, C. / Ginn, H.M. / Jackson, T. / PerezMartin, E. ...Kotecha, A. / Seago, J. / Scott, K. / Burman, A. / Loureiro, S. / Ren, J. / Porta, C. / Ginn, H.M. / Jackson, T. / PerezMartin, 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.
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 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Oct 21, 2015Group: Database references
Revision 1.3Aug 30, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.image_processing_id / _em_software.name
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-3129
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  • Superimposition on EM map
  • EMDB-3129
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Structure viewerMolecule:
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Assembly

Deposited unit
1: VP1
2: VP3
3: VP2
4: VP4


Theoretical massNumber of molelcules
Total (without water)79,9834
Polymers79,9834
Non-polymers00
Water00
1
1: VP1
2: VP3
3: VP2
4: VP4
x 60


Theoretical massNumber of molelcules
Total (without water)4,799,002240
Polymers4,799,002240
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: VP1
2: VP3
3: VP2
4: VP4
x 5


  • icosahedral pentamer
  • 400 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)399,91720
Polymers399,91720
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
1: VP1
2: VP3
3: VP2
4: VP4
x 6


  • icosahedral 23 hexamer
  • 480 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)479,90024
Polymers479,90024
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
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein VP1 / FOOT-AND-MOUTH DISEASE VIRUS


Mass: 22865.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FOOT-AND-MOUTH DISEASE VIRUS / Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS - TYPE O / Cell line (production host): BHK-21 / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: Q6PMW3
#2: Protein VP3 / FOOT-AND-MOUTH DISEASE VIRUS


Mass: 24417.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FOOT-AND-MOUTH DISEASE VIRUS / Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS - TYPE O / Cell line (production host): BHK-21 / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: Q6PMW3
#3: Protein VP2 / FOOT-AND-MOUTH DISEASE VIRUS


Mass: 23933.879 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: FMDV O1 MANISA SEROTYPE WITH A MUTATION AT VP2 S93Y
Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS - TYPE O / Cell line (production host): BHK-21 / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: Q6PMW3
#4: Protein VP4 / FOOT-AND-MOUTH DISEASE VIRUS


Mass: 8766.075 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: FOOT-AND-MOUTH DISEASE VIRUS / Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS - TYPE O / Cell line (production host): BHK-21 / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: Q6PMW3
Sequence detailsONE MUTATION S93Y ON VP2

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: INACTIVATED FMDV O1M PARTICLE, STABILISED MUTANT / Type: VIRUS
Buffer solutionName: 50MM HEPES PH 8.0, 200 MM NACL / pH: 8 / Details: 50MM HEPES PH 8.0, 200 MM NACL
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 70, TEMPERATURE- 120, INSTRUMENT- FEI VITROBOT MARK IV, METHOD- BLOT FOR 3 SECONDS BEFORE PLUNGING,

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Jun 22, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 160000 X / Calibrated magnification: 37037 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Image scansNum. digital images: 418

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Processing

EM softwareName: RELION / Category: 3D reconstruction
CTF correctionDetails: INDIVIDUAL PARTICLES
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 3.2 Å / Num. of particles: 8267 / Actual pixel size: 1.35 Å
Magnification calibration: CROSS- -CORRELATION AGAINST ATOMIC MODEL
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3129. (DEPOSITION ID: 13685).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--LOCAL CORRELATION FOLLOWED BY RIGIDBODY AND REAL SPACE REFINEMENT REFINEMENT PROTOCOL--CRYOEM
RefinementHighest resolution: 3.2 Å
Refinement stepCycle: LAST / Highest resolution: 3.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5115 0 0 0 5115

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