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

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Entry
Database: EMDB / ID: 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.
SampleSputnik:
virus
KeywordsVirophage / Mimivirus / PRD1-adenovirus lineage
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
SourceSputnik virophage (Sputnik)
Methodsingle particle reconstruction / cryo EM / 10.6 Å resolution
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
Validation ReportPDB-ID: 3kk5

SummaryFull reportAbout validation report
DateDeposition: Nov 4, 2009 / Header (metadata) release: Jan 8, 2010 / Map release: Jan 8, 2010 / Last update: Apr 16, 2014

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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
  • Download
  • 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 models: PDB-3kk5
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_1662.map.gz (map file in CCP4 format, 1024001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
640 pix
1.62 Å/pix.
= 1036.8 Å
640 pix
1.62 Å/pix.
= 1036.8 Å
640 pix
1.62 Å/pix.
= 1036.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.62 Å
Density
Contour Level:2.0 (by author), 1 (movie #1):
Minimum - Maximum-5.2826 - 8.17328
Average (Standard dev.)0.0357989 (0.992055)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions640640640
Origin-320-320-320
Limit319319319
Spacing640640640
CellA=B=C: 1036.8 Å
α=β=γ: 90 deg.

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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Others

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Sample components

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Entire Sputnik

EntireName: Sputnik / Details: 1mg per ml concentration / Number of components: 1

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Component #1: virus, Sputnik virophage

VirusName: Sputnik virophage / a.k.a: Sputnik / Class: SATELLITE / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Sputnik virophage (Sputnik)
Source (natural)Host Species: Acanthamoeba polyphaga (eukaryote) / Host category: PROTOZOA
Shell #1Name of element: gp20 / Diameter: 730 Å / T number(triangulation number): 27

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: PBS / pH: 7.4
Support filmHoley grids
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 90 K / Method: 3.5ul of sample hand blotted approx. 1sec
Details: Vitrification instrument: In-house, gravity driven plunger

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 38000 X (nominal), 39190 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 767 - 3582 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN

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Image acquisition

Image acquisitionNumber of digital images: 115 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 6780 / Applied symmetry: I (icosahedral)
3D reconstructionSoftware: EMAN / CTF correction: Each micrograph / Resolution: 10.6 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: EMFIT / Refinement protocol: rigid body / Refinement space: REAL / Details: Protocol: Rigid Body
Input PDB model: 1M3Y
Output model

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