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- PDB-3j26: The 3.5 A resolution structure of the Sputnik virophage by cryo-EM -

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Basic information

Entry
Database: PDB / ID: 3j26
TitleThe 3.5 A resolution structure of the Sputnik virophage by cryo-EM
Components
  • Minor virion protein
  • capsid protein V20
KeywordsVIRUS / double jelly-roll / single jelly-roll
Function / homologyJelly Rolls - #1100 / viral capsid / Jelly Rolls / Sandwich / Mainly Beta / Putative capsid protein V20 / Minor virion protein
Function and homology information
Biological speciesSputnik virophage (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang, X.Z.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Structure of Sputnik, a virophage, at 3.5-Å resolution.
Authors: Xinzheng Zhang / Siyang Sun / Ye Xiang / Jimson Wong / Thomas Klose / Didier Raoult / Michael G Rossmann /
Abstract: "Sputnik" is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. We have used cryo-EM to produce an electron density map of the icosahedral Sputnik virus ..."Sputnik" is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. We have used cryo-EM to produce an electron density map of the icosahedral Sputnik virus at 3.5-Å resolution, sufficient to verify the identity of most amino acids in the capsid proteins and to establish the identity of the pentameric protein forming the fivefold vertices. It was also shown that the virus lacks an internal membrane. The capsid is organized into a T = 27 lattice in which there are 260 trimeric capsomers and 12 pentameric capsomers. The trimeric capsomers consist of three double "jelly-roll" major capsid proteins creating pseudohexameric capsomer symmetry. The pentameric capsomers consist of five single jelly-roll proteins. The release of the genome by displacing one or more of the pentameric capsomers may be the result of a low-pH environment. These results suggest a mechanism of Sputnik DNA ejection that probably also occurs in other big icosahedral double jelly-roll viruses such as Adenovirus. In this study, the near-atomic resolution structure of a virus has been established where crystallization for X-ray crystallography was not feasible.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3Jul 17, 2013Group: Other
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.5Feb 21, 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
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  • Superimposition on EM map
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  • Superimposition on EM map
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: capsid protein V20
B: capsid protein V20
C: capsid protein V20
D: capsid protein V20
E: capsid protein V20
F: capsid protein V20
G: capsid protein V20
H: capsid protein V20
I: capsid protein V20
J: capsid protein V20
K: capsid protein V20
L: capsid protein V20
M: capsid protein V20
N: Minor virion protein


Theoretical massNumber of molelcules
Total (without water)773,89714
Polymers773,89714
Non-polymers00
Water00
1
A: capsid protein V20
B: capsid protein V20
C: capsid protein V20
D: capsid protein V20
E: capsid protein V20
F: capsid protein V20
G: capsid protein V20
H: capsid protein V20
I: capsid protein V20
J: capsid protein V20
K: capsid protein V20
L: capsid protein V20
M: capsid protein V20
N: Minor virion protein
x 60


Theoretical massNumber of molelcules
Total (without water)46,433,822840
Polymers46,433,822840
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: capsid protein V20
B: capsid protein V20
C: capsid protein V20
D: capsid protein V20
E: capsid protein V20
F: capsid protein V20
G: capsid protein V20
H: capsid protein V20
I: capsid protein V20
J: capsid protein V20
K: capsid protein V20
L: capsid protein V20
M: capsid protein V20
N: Minor virion protein
x 5


  • icosahedral pentamer
  • 3.87 MDa, 70 polymers
Theoretical massNumber of molelcules
Total (without water)3,869,48570
Polymers3,869,48570
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: capsid protein V20
B: capsid protein V20
C: capsid protein V20
D: capsid protein V20
E: capsid protein V20
F: capsid protein V20
G: capsid protein V20
H: capsid protein V20
I: capsid protein V20
J: capsid protein V20
K: capsid protein V20
L: capsid protein V20
M: capsid protein V20
N: Minor virion protein
x 6


  • icosahedral 23 hexamer
  • 4.64 MDa, 84 polymers
Theoretical massNumber of molelcules
Total (without water)4,643,38284
Polymers4,643,38284
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
capsid protein V20 / major capsid protein


Mass: 56245.621 Da / Num. of mol.: 13 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Sputnik virophage (virus) / References: UniProt: B4YNG0
#2: Protein Minor virion protein / penton protein


Mass: 42703.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sputnik virophage (virus) / References: UniProt: I0CES9
Sequence detailsFULL-LENGTH CAPSID PROTEIN V20 (MAJOR CAPSID PROTEIN) WAS PRESENT IN THE SAMPLE, BUT ONLY UNP ...FULL-LENGTH CAPSID PROTEIN V20 (MAJOR CAPSID PROTEIN) WAS PRESENT IN THE SAMPLE, BUT ONLY UNP RESIDUES 1-508 WERE MODELED.

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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: Sputnik virus / Type: VIRUS
Details of virusEmpty: NO / Enveloped: NO / Host category: EUKARYOTE / Isolate: STRAIN / Type: SATELLITE
Natural hostOrganism: Acanthamoeba
Buffer solutionName: PBS / pH: 7 / Details: PBS
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh copper grid with 1.2 um holes
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temp: 100 K / Humidity: 90 %
Details: 6 second blot, plunged into liquid ethane (GATAN CRYOPLUNGE 3)
Method: 6 second blot

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Jan 1, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm
Specimen holderTemperature: 100 K
Image recordingElectron dose: 22 e/Å2 / Film or detector model: KODAK SO-163 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
1EMAN3D reconstruction
2FREALIGN3D reconstruction
CTF correctionDetails: each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: projection matching / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12000 / Actual pixel size: 1.1 Å / Symmetry type: POINT
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms54479 0 0 0 54479

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