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- PDB-3kk5: Crystal structure of PBCV-1 VP54 fitted into a cryo-EM reconstruc... -

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Basic information

Entry
Database: PDB / ID: 3kk5
TitleCrystal structure of PBCV-1 VP54 fitted into a cryo-EM reconstruction of the virophage Sputnik
ComponentsMajor capsid protein
KeywordsVIRUS / double jellyroll / Capsid protein / Late protein / Virion / Icosahedral virus
Function / homologyMajor capsid protein, C-terminal / Hexon coat protein, subdomain 4 / Group II dsDNA virus coat/capsid protein / Major capsid protein, N-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Major capsid protein N-terminus / viral capsid / structural molecule activity / Major capsid protein
Function and homology information
Specimen sourceAcanthamoeba polyphaga (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 10.6 Å resolution
AuthorsSun, S. / Rossmann, M.G.
CitationJournal: J. Virol. / Year: 2010
Title: Structural studies of the Sputnik virophage.
Authors: Siyang Sun / Bernard La Scola / Valorie D Bowman / Christopher M Ryan / Julian P Whitelegge / Didier Raoult / Michael G Rossmann
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 4, 2009 / Release: Nov 17, 2009
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 17, 2009Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance
1.2Jan 24, 2018Structure modelData collection / Data processing / Structure summaryaudit_author / em_image_scans / em_software_audit_author.name / _em_software.name
1.3Jul 18, 2018Structure modelData collectionem_software_em_software.image_processing_id

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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
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-1662
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  • Superimposition on EM map
  • EMDB-1662
  • Imaged by UCSF Chimera
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)626,59513
Polyers626,59513
Non-polymers00
Water0
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)37,595,708780
Polyers37,595,708780
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
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
x 5


  • icosahedral pentamer
  • 3.13 MDa, 65 polymers
Theoretical massNumber of molelcules
Total (without water)3,132,97665
Polyers3,132,97665
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
K: Major capsid protein
L: Major capsid protein
M: Major capsid protein
x 6


  • icosahedral 23 hexamer
  • 3.76 MDa, 78 polymers
Theoretical massNumber of molelcules
Total (without water)3,759,57178
Polyers3,759,57178
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
Major capsid protein / MCP / VP54 / Coordinate model: Cα atoms only


Mass: 48199.625 Da / Num. of mol.: 13 / Source: (natural) Acanthamoeba polyphaga (eukaryote) / References: UniProt: P30328

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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: major capsid protein of sputnik
Details of virusVirus host category: PROTOZOA / Virus isolate: SPECIES / Virus type: SATELLITE
Natural hostOrganism: Acanthamoeba polyphaga
Buffer solutionName: PBS / Details: PBS / pH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: flash-frozen on holey grids in liquid ethane

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 38000 / Calibrated magnification: 39190 / Nominal defocus max: 3582 nm / Nominal defocus min: 767 nm / Cs: 2 mm
Specimen holderTemperature: 70 kelvins
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EMfitmodel fitting
2EMAN3D reconstruction
CTF correctionDetails: CTF parameters were calculated for particles in each micrograph.
SymmetryPoint symmetry: I
3D reconstructionMethod: projection matching / Resolution: 10.6 Å / Number of particles: 6780 / Nominal pixel size: 1.62 / Actual pixel size: 1.62 / Details: EMAN / Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--rigid body / Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Sumf
Atomic model buildingPDB-ID: 1M3Y
Number of atoms included #LASTProtein: 5369 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 5369

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