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- EMDB-5495: Cryo-EM reconstruction of Sputnik virus -

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Basic information

Entry
Database: EMDB / ID: EMD-5495
TitleCryo-EM reconstruction of Sputnik virus
Map dataReconstruction of Sputnik virus full particles at 3.5A resolution
Sample
  • Sample: Sputnik
  • Virus: Sputnik virophage (virus)
KeywordsJelly roll structure / major capsid protein / penton protein / minor capsid protein
Function / homology
Function and homology information


: / : / : / Sputnik minor capsid protein V18/19 / Sputnik virophage major capsid protein 1st domain / : / Major capsid protein V20 C-terminal domain
Similarity search - Domain/homology
Putative capsid protein V20 / Minor virion protein
Similarity search - Component
Biological speciesSputnik virophage (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsZhang XZ / Sun SY / Xiang Y / Wong J / Klose T / Raoult D / Rossmann MG
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 12, 2012-
Header (metadata) releaseSep 26, 2012-
Map releaseOct 24, 2012-
UpdateNov 14, 2012-
Current statusNov 14, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j26
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j26
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j26
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5495_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5495.map.gz / Format: CCP4 / Size: 843.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Sputnik virus full particles at 3.5A resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 768 pix.
= 844.8 Å		1.1 Å/pix.
x 768 pix.
= 844.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-2.14440989 - 21.699911119999999
Average (Standard dev.)0.10871017 (±1.24200082)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-384-3840
Dimensions768768384
Spacing768768384
CellA: 844.80005 Å / B: 844.80005 Å / C: 422.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z768768384
origin x/y/z0.0000.0000.000
length x/y/z844.800844.800422.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-384-3840
NC/NR/NS768768384
D min/max/mean-2.14421.7000.109

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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 / Number unique components: 1

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Supramolecule #1: Sputnik virophage

SupramoleculeName: Sputnik virophage / type: virus / ID: 1 / Details: Sputnik virus full particle / NCBI-ID: 543939 / Sci species name: Sputnik virophage / Database: NCBI / Virus type: SATELLITE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Acanthamoeba (eukaryote) / synonym: PROTOZOA
Virus shellShell ID: 1 / Name: Vp20 / Diameter: 750 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 / Details: PBS
GridDetails: 400 mesh Cu grid (c-flat), 1.2 um hole, glow discharged
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 100 K / Instrument: GATAN CRYOPLUNGE 3 / Method: blot 6 seconds

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Alignment procedureLegacy - Astigmatism: corrected at 250,000 magnification
DateJan 1, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Average electron dose: 22 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsUsing EMAN
CTF correctionDetails: each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN, Frealign / Number images used: 12000
Final angle assignmentDetails: EMAN

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