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- EMDB-1662: Structural Studies of the Sputnik Virophage -

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Basic information

Entry
Database: EMDB / ID: EMD-1662
TitleStructural Studies of the Sputnik Virophage
Map dataThis is a map of an icosahedral reconstruction of Sputnik low pass filtered to 10A and sharpened with a structure factor file.
Sample
  • Sample: Sputnik
  • Virus: Sputnik virophage (virus)
KeywordsVirophage / Mimivirus / PRD1-adenovirus lineage
Function / homology
Function and homology information


viral capsid / lipid binding / structural molecule activity
Similarity search - Function
Major 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
Similarity search - Domain/homology
Major capsid protein
Similarity search - Component
Biological speciesSputnik virophage (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.6 Å
AuthorsSun S / Scola BL / Bowman VD / Ryan CM / Whitelegge JP / Raoult D / Rossmann MG
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, 2009-
Header (metadata) releaseJan 8, 2010-
Map releaseJan 8, 2010-
UpdateApr 16, 2014-
Current statusApr 16, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3kk5
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3kk5
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3kk5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol

Downloads & links

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Map

FileDownload / File: emd_1662.map.gz / Format: CCP4 / Size: 976.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of an icosahedral reconstruction of Sputnik low pass filtered to 10A and sharpened with a structure factor file.
Voxel sizeX=Y=Z: 1.62 Å
Density
Contour LevelBy AUTHOR: 2.0 / Movie #1: 1
Minimum - Maximum-5.2826 - 8.17328
Average (Standard dev.)0.0357989 (±0.992055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-320-320-320
Dimensions640640640
Spacing640640640
CellA=B=C: 1036.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.621.621.62
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z1036.8001036.8001036.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-147
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS-320-320-320
NC/NR/NS640640640
D min/max/mean-5.2838.1730.036

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Supplemental data

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Sample components

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Entire : Sputnik

EntireName: Sputnik
Components
  • Sample: Sputnik
  • Virus: Sputnik virophage (virus)

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Supramolecule #1000: Sputnik

SupramoleculeName: Sputnik / type: sample / ID: 1000 / Details: 1mg per ml concentration / Number unique components: 1

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Supramolecule #1: Sputnik virophage

SupramoleculeName: Sputnik virophage / type: virus / ID: 1 / Name.synonym: Sputnik / NCBI-ID: 543939 / Sci species name: Sputnik virophage / Virus type: SATELLITE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Sputnik
Host (natural)Organism: Acanthamoeba polyphaga (eukaryote) / synonym: PROTOZOA
Virus shellShell ID: 1 / Name: gp20 / Diameter: 730 Å / T number (triangulation number): 27

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.4 / Details: PBS
GridDetails: Holey grids
VitrificationCryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: In-house, gravity driven plunger
Method: 3.5ul of sample hand blotted approx. 1sec

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Image recordingDigitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 115 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 39190 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.582 µm / Nominal defocus min: 0.767 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 10.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 6780

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Atomic model buiding 1

Initial modelPDB ID:

1m3y
PDB Unreleased entry

SoftwareName: EMFIT
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3kk5:
Crystal structure of PBCV-1 VP54 fitted into a cryo-EM reconstruction of the virophage Sputnik

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