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

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Entry
Database: PDB / ID: 5aca
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 / homologyHelicase/polymerase/peptidase polyprotein, Calicivirus-type / P-loop containing nucleoside triphosphate hydrolase / Foot-and-mouth disease virus VP1 coat / RNA-directed RNA polymerase, catalytic domain / Peptidase C28, foot-and-mouth virus L-proteinase / Peptidase S1, PA clan / Helicase, superfamily 3, single-stranded RNA virus / Capsid protein VP4, Picornavirus / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain ...Helicase/polymerase/peptidase polyprotein, Calicivirus-type / P-loop containing nucleoside triphosphate hydrolase / Foot-and-mouth disease virus VP1 coat / RNA-directed RNA polymerase, catalytic domain / Peptidase C28, foot-and-mouth virus L-proteinase / Peptidase S1, PA clan / Helicase, superfamily 3, single-stranded RNA virus / Capsid protein VP4, Picornavirus / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Picornavirus/Calicivirus coat protein / Capsid protein VP4 superfamily, Picornavirus / Papain-like cysteine peptidase superfamily / picornavirus capsid protein / 3C cysteine protease (picornain 3C) / RNA dependent RNA polymerase / RNA helicase / Picornavirus capsid / Helicase, superfamily 3, single-stranded DNA/RNA virus / Viral protein VP4 subunit / Peptidase C3A/C3B, picornaviral / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Foot-and-mouth virus L-proteinase / icosahedral viral capsid / host cell cytoplasmic vesicle membrane / viral protein processing / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / ion channel activity / protein complex oligomerization / viral RNA genome replication / viral entry into host cell / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding / p1 polyprotein / Genome polyprotein
Function and homology information
Specimen sourceFOOT-AND-MOUTH DISEASE VIRUS - TYPE SAT 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.5 Å resolution
AuthorsKotecha, 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.
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 / Guntram Paul / Juha T Huiskonen / Ian M Jones / Robert M Esnouf / Elizabeth E Fry / Francois F Maree / Bryan Charleston / David I Stuart
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 14, 2015 / Release: Sep 23, 2015
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 23, 2015Structure modelrepositoryInitial release
1.1Sep 30, 2015Structure modelDatabase references
1.2Oct 21, 2015Structure modelDatabase references
1.3Aug 30, 2017Structure modelData collection / Refinement descriptionem_3d_fitting / em_software_em_3d_fitting.target_criteria / _em_software.image_processing_id / _em_software.name

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-3130
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  • Superimposition on EM map
  • EMDB-3130
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,8434
Polyers80,8434
Non-polymers00
Water0
1
1: VP1
2: VP2
3: VP3
4: VP4
x 60


Theoretical massNumber of molelcules
Total (without water)4,850,568240
Polyers4,850,568240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
1: VP1
2: VP2
3: VP3
4: VP4
x 5


  • icosahedral pentamer
  • 404 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)404,21420
Polyers404,21420
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: VP1
2: VP2
3: VP3
4: VP4
x 6


  • icosahedral 23 hexamer
  • 485 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)485,05724
Polyers485,05724
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Protein/peptide VP1


Mass: 24160.209 Da / Num. of mol.: 1
Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS - TYPE SAT 2
Cell line (production host): BHK-21 / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: Q1L764, UniProt: Q719N0*PLUS
#2: Protein/peptide VP2


Mass: 23226.023 Da / Num. of mol.: 1 / Details: FMDV SAT2 SEROTYPE WITH A MUTATION AT VP2 S93Y / Mutation: YES
Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS - TYPE SAT 2
Cell line (production host): BHK-21 / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: Q1L764, UniProt: Q719N0*PLUS
#3: Protein/peptide VP3


Mass: 24620.328 Da / Num. of mol.: 1
Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS - TYPE SAT 2
Cell line (production host): BHK-21 / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: Q1L764
#4: Protein/peptide VP4


Mass: 8836.233 Da / Num. of mol.: 1
Source: (gene. exp.) FOOT-AND-MOUTH DISEASE VIRUS - TYPE SAT 2
Cell line (production host): BHK-21 / Production host: MESOCRICETUS AURATUS (golden hamster) / References: UniProt: Q1L764
Sequence detailsVP2 S93Y

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: INACTIVATED FMDV SAT2 PARTICLE, STABILISED MUTANT / Type: VIRUS
Buffer solutionName: 50MM HEPES PH 8.0, 200 MM NACL / Details: 50MM HEPES PH 8.0, 200 MM NACL / pH: 8
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
MicroscopyMicroscope model: FEI TECNAI F30 / Date: May 11, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 160000 / Calibrated magnification: 37037 / 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 scansNumber digital images: 628

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Processing

EM softwareName: RELION / Category: 3D reconstruction
CTF correctionDetails: EACH PARTICLE
SymmetryPoint symmetry: I
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 3.5 Å / Number of particles: 8156 / Actual pixel size: 1.35
Magnification calibration: CROSS- -CORRELATION AGAINST ATOMIC MODEL
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3130. (DEPOSITION ID: 13687).
Symmetry type: POINT
Atomic model buildingDetails: METHOD--LOCAL CORRELATION FOLLOWED BY RIGIDBODY AND REAL SPACE REFINEMENT REFINEMENT PROTOCOL--CRYOEM
Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Cross-correlation coefficient
Least-squares processHighest resolution: 3.5 Å
Refine hist #LASTHighest resolution: 3.5 Å
Number of atoms included #LASTProtein: 5244 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 5244

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