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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 / homologyviral capsid / Putative capsid protein V20 / Minor virion protein
Function and homology information
Specimen sourceSputnik virophage (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.5 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Sep 18, 2012 / Release: Oct 24, 2012
RevisionDateData content typeGroupCategoryItemProviderType
1.0Oct 24, 2012Structure modelrepositoryInitial release
1.1Oct 31, 2012Structure modelDatabase references
1.2Nov 14, 2012Structure modelDatabase references
1.3Jul 17, 2013Structure modelOther
1.4Jul 18, 2018Structure modelData collectionem_image_scans / em_software_em_software.image_processing_id / _em_software.name

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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-5495
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  • Superimposition on EM map
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Structure viewerMolecule:
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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
Polyers773,89714
Non-polymers00
Water0
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
Polyers46,433,822840
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: 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
Polyers3,869,48570
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
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
Polyers4,643,38284
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
capsid protein V20 / / major capsid protein


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


Mass: 42703.965 Da / Num. of mol.: 1 / 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 / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Sputnik virus / Type: VIRUS
Details of virusEmpty: NO / Enveloped: NO / Virus host category: EUKARYOTE / Virus isolate: STRAIN / Virus type: SATELLITE
Natural hostOrganism: Acanthamoeba
Buffer solutionName: PBS / Details: PBS / pH: 7
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
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Jan 1, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 / Nominal defocus max: 2400 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm
Specimen holderTemperature: 100 kelvins
Image recordingElectron dose: 22 e/Å2 / Film or detector model: KODAK SO-163 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
1EMAN3D reconstruction
2FREALIGN3D reconstruction
CTF correctionDetails: each particle
SymmetryPoint symmetry: I
3D reconstructionMethod: projection matching / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 12000 / Actual pixel size: 1.1 / Symmetry type: POINT
Number of atoms included #LASTProtein: 54479 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 54479

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