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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, N-terminal / Major capsid protein N-terminus / Major capsid protein, C-terminal / Major capsid protein, C-terminal domain superfamily / Large eukaryotic DNA virus major capsid protein / Group II dsDNA virus coat/capsid protein / viral capsid / structural molecule activity / Major capsid protein
Function and homology information
Biological speciesAcanthamoeba polyphaga (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.6 Å
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 /
Abstract: The virophage Sputnik is a satellite virus of the giant mimivirus and is the only satellite virus reported to date whose propagation adversely affects its host virus' production. Genome sequence ...The virophage Sputnik is a satellite virus of the giant mimivirus and is the only satellite virus reported to date whose propagation adversely affects its host virus' production. Genome sequence analysis showed that Sputnik has genes related to viruses infecting all three domains of life. Here, we report structural studies of Sputnik, which show that it is about 740 A in diameter, has a T=27 icosahedral capsid, and has a lipid membrane inside the protein shell. Structural analyses suggest that the major capsid protein of Sputnik is likely to have a double jelly-roll fold, although sequence alignments do not show any detectable similarity with other viral double jelly-roll capsid proteins. Hence, the origin of Sputnik's capsid might have been derived from other viruses prior to its association with mimivirus.
History
DepositionNov 4, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Data collection / Data processing / Structure summary
Category: audit_author / em_image_scans / em_software / Item: _audit_author.name / _em_software.name
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.4Feb 21, 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 / em_3d_fitting_list / 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 / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • 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
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  • Superimposition on EM map
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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
Polymers626,59513
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
Polymers37,595,708780
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
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
Polymers3,132,97665
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
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
Polymers3,759,57178
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
Major capsid protein / MCP / VP54 / Coordinate model: Cα atoms only


Mass: 48199.625 Da / Num. of mol.: 13 / Source method: isolated from a natural source / 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 / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: major capsid protein of sputnik
Details of virusHost category: PROTOZOA / Isolate: SPECIES / Type: SATELLITE
Natural hostOrganism: Acanthamoeba polyphaga
Buffer solutionName: PBS / pH: 7.4 / Details: PBS
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

MicroscopyModel: 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 X / Calibrated magnification: 39190 X / Nominal defocus max: 3582 nm / Nominal defocus min: 767 nm / Cs: 2 mm
Specimen holderTemperature: 70 K
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GENERIC FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (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 (icosahedral)
3D reconstructionMethod: projection matching / Resolution: 10.6 Å / Num. of particles: 6780 / Nominal pixel size: 1.62 Å / Actual pixel size: 1.62 Å / Details: EMAN / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Sumf / Details: REFINEMENT PROTOCOL--rigid body
Atomic model buildingPDB-ID: 1M3Y

1m3y
PDB Unreleased entry


Accession code: 1M3Y / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms5369 0 0 0 5369

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