EMDB-1662: Structural Studies of the Sputnik Virophage

Basic information

• Entry: Database: EMDB / ID: EMD-1662
• Title: Structural Studies of the Sputnik Virophage
• Map data: This 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)

• Keywords: Virophage / Mimivirus / PRD1-adenovirus lineage
• Function / homology: 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 / viral capsid / structural molecule activity / Major capsid protein
• Biological species: Sputnik virophage (virus)
• Method: single particle reconstruction / cryo EM / Resolution: 10.6 Å
• Authors: Sun S / Scola BL / Bowman VD / Ryan CM / Whitelegge JP / Raoult D / Rossmann MG
• Citation: Journal: 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 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

Deposition	Nov 4, 2009	-
Header (metadata) release	Jan 8, 2010	-
Map release	Jan 8, 2010	-
Update	Apr 16, 2014	-
Current status	Apr 16, 2014	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_1662.map.gz / Format: CCP4 / Size: 976.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Annotation: This is a map of an icosahedral reconstruction of Sputnik low pass filtered to 10A and sharpened with a structure factor file.
• Voxel size: X=Y=Z: 1.62 Å

Density

Contour Level	By AUTHOR: 2.0 / Movie #1: 1
Minimum - Maximum	-5.2826 - 8.17328
Average (Standard dev.)	0.0357989 (±0.992055)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin -320 -320 -320 Dimensions 640 640 640 Spacing 640 640 640
Cell	A=B=C: 1036.8 Å α=β=γ: 90 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.62	1.62	1.62
M x/y/z	640	640	640
origin x/y/z	0.000	0.000	0.000
length x/y/z	1036.800	1036.800	1036.800
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	-147	-147	-147
NX/NY/NZ	294	294	294
MAP C/R/S	1	2	3
start NC/NR/NS	-320	-320	-320
NC/NR/NS	640	640	640
D min/max/mean	-5.283	8.173	0.036

Supplemental data

Others

• Details: [pdb_fitting_matrix.txt]; matrix 1; 1.0000 0.0000 0.0000 0.0000; 0.0000 1.0000 0.0000 0.0000; 0.0000 0.0000 1.0000 0.0000; matrix 2; 0.3090 -0.5000 0.8090 0.0000; 0.5000 0.8090 0.3090 0.0000; -0.8090 0.3090 0.5000 0.0000; matrix 3 ; -0.8090 -0.3090 0.5000 0.0000; 0.3090 0.5000 0.8090 0.0000; -0.5000 0.8090 -0.3090 0.0000; matrix 4; -0.8090 0.3090 -0.5000 0.0000; -0.3090 0.5000 0.8090 0.0000; 0.5000 0.8090 -0.3090 0.0000; matrix 5; 0.3090 0.5000 -0.8090 0.0000; -0.5000 0.8090 0.3090 0.0000; 0.8090 0.3090 0.5000 0.0000; matrix 6; -0.5000 -0.8090 -0.3090 0.0000; -0.8090 0.3090 0.5000 0.0000; -0.3090 0.5000 -0.8090 0.0000; matrix 7; -0.3090 -0.5000 -0.8090 0.0000; -0.5000 0.8090 -0.3090 0.0000; 0.8090 0.3090 -0.5000 0.0000; matrix 8; 0.3090 -0.5000 -0.8090 0.0000; 0.5000 0.8090 -0.3090 0.0000; 0.8090 -0.3090 0.5000 0.0000; matrix 9; 0.5000 -0.8090 -0.3090 0.0000; 0.8090 0.3090 0.5000 0.0000; -0.3090 -0.5000 0.8090 0.0000; matrix 10; 0.0000 -1.0000 0.0000 0.0000; 0.0000 0.0000 1.0000 0.0000; -1.0000 0.0000 0.0000 0.0000; matrix 11; -0.5000 -0.8090 0.3090 0.0000; -0.8090 0.3090 -0.5000 0.0000; 0.3090 -0.5000 -0.8090 0.0000; matrix 12; -0.8090 -0.3090 -0.5000 0.0000; 0.3090 0.5000 -0.8090 0.0000; 0.5000 -0.8090 -0.3090 0.0000; matrix 13; 0.0000 0.0000 -1.0000 0.0000; 1.0000 0.0000 0.0000 0.0000; 0.0000 -1.0000 0.0000 0.0000; matrix 14; 0.8090 -0.3090 -0.5000 0.0000; 0.3090 -0.5000 0.8090 0.0000; -0.5000 -0.8090 -0.3090 0.0000; matrix 15; 0.5000 -0.8090 0.3090 0.0000; -0.8090 -0.3090 0.5000 0.0000; -0.3090 -0.5000 -0.8090 0.0000; matrix 16; 0.8090 0.3090 -0.5000 0.0000; 0.3090 0.5000 0.8090 0.0000; 0.5000 -0.8090 0.3090 0.0000; matrix 17; 0.8090 -0.3090 0.5000 0.0000; -0.3090 0.5000 0.8090 0.0000; -0.5000 -0.8090 0.3090 0.0000; matrix 18; -0.3090 -0.5000 0.8090 0.0000; -0.5000 0.8090 0.3090 0.0000; -0.8090 -0.3090 -0.5000 0.0000; matrix 19; -1.0000 0.0000 0.0000 0.0000; 0.0000 1.0000 0.0000 0.0000; 0.0000 0.0000 -1.0000 0.0000; matrix 20; -0.3090 0.5000 -0.8090 0.0000; 0.5000 0.8090 0.3090 0.0000; 0.8090 -0.3090 -0.5000 0.0000; matrix 21; 0.0000 0.0000 1.0000 0.0000; 1.0000 0.0000 0.0000 0.0000; 0.0000 1.0000 0.0000 0.0000; matrix 22; 0.0000 1.0000 0.0000 0.0000; 0.0000 0.0000 1.0000 0.0000; 1.0000 0.0000 0.0000 0.0000; matrix 23; -0.8090 0.3090 0.5000 0.0000; 0.3090 -0.5000 0.8090 0.0000; 0.5000 0.8090 0.3090 0.0000; matrix 24; 0.5000 0.8090 0.3090 0.0000; -0.8090 0.3090 0.5000 0.0000; 0.3090 -0.5000 0.8090 0.0000; matrix 25; -0.5000 0.8090 -0.3090 0.0000; -0.8090 -0.3090 0.5000 0.0000; 0.3090 0.5000 0.8090 0.0000; matrix 26; 0.3090 0.5000 0.8090 0.0000; -0.5000 0.8090 -0.3090 0.0000; -0.8090 -0.3090 0.5000 0.0000; matrix 27; 0.5000 0.8090 -0.3090 0.0000; -0.8090 0.3090 -0.5000 0.0000; -0.3090 0.5000 0.8090 0.0000; matrix 28; -0.3090 0.5000 0.8090 0.0000; 0.5000 0.8090 -0.3090 0.0000; -0.8090 0.3090 -0.5000 0.0000; matrix 29; 0.8090 0.3090 0.5000 0.0000; 0.3090 0.5000 -0.8090 0.0000; -0.5000 0.8090 0.3090 0.0000; matrix 30; -0.5000 0.8090 0.3090 0.0000; 0.8090 0.3090 0.5000 0.0000; 0.3090 0.5000 -0.8090 0.0000; matrix 31; -0.3090 0.5000 -0.8090 0.0000; -0.5000 -0.8090 -0.3090 0.0000; -0.8090 0.3090 0.5000 0.0000; matrix 32; -0.8090 0.3090 0.5000 0.0000; -0.3090 0.5000 -0.8090 0.0000; -0.5000 -0.8090 -0.3090 0.0000; matrix 33; 0.8090 0.3090 -0.5000 0.0000; -0.3090 -0.5000 -0.8090 0.0000; -0.5000 0.8090 -0.3090 0.0000; matrix 34; -0.5000 0.8090 -0.3090 0.0000; 0.8090 0.3090 -0.5000 0.0000; -0.3090 -0.5000 -0.8090 0.0000; matrix 35; 0.8090 -0.3090 0.5000 0.0000; 0.3090 -0.5000 -0.8090 0.0000; 0.5000 0.8090 -0.3090 0.0000; matrix 36; 0.5000 0.8090 -0.3090 0.0000; 0.8090 -0.3090 0.5000 0.0000; 0.3090 -0.5000 -0.8090 0.0000; matrix 37; -0.3090 -0.5000 0.8090 0.0000; 0.5000 -0.8090 -0.3090 0.0000; 0.8090 0.3090 0.5000 0.0000; matrix 38; 0.8090 0.3090 0.5000 0.0000; -0.3090 -0.5000 0.8090 0.0000; 0.5000 -0.8090 -0.3090 0.0000; matrix 39; -1.0000 0.0000 0.0000 0.0000; 0.0000 -1.0000 0.0000 0.0000; 0.0000 0.0000 1.0000 0.0000; matrix 40; 0.0000 0.0000 1.0000 0.0000; -1.0000 0.0000 0.0000 0.0000; 0.0000 -1.0000 0.0000 0.0000; matrix 41; 0.3090 -0.5000 -0.8090 0.0000; -0.5000 -0.8090 0.3090 0.0000; -0.8090 0.3090 -0.5000 0.0000; matrix 42; -0.8090 0.3090 -0.5000 0.0000; 0.3090 -0.5000 -0.8090 0.0000; -0.5000 -0.8090 0.3090 0.0000; matrix 43; 0.5000 -0.8090 -0.3090 0.0000; -0.8090 -0.3090 -0.5000 0.0000; 0.3090 0.5000 -0.8090 0.0000; matrix 44; 0.3090 0.5000 -0.8090 0.0000; 0.5000 -0.8090 -0.3090 0.0000; -0.8090 -0.3090 -0.5000 0.0000; matrix 45; 0.0000 -1.0000 0.0000 0.0000; 0.0000 0.0000 -1.0000 0.0000; 1.0000 0.0000 0.0000 0.0000; matrix 46; 1.0000 0.0000 0.0000 0.0000; 0.0000 -1.0000 0.0000 0.0000; 0.0000 0.0000 -1.0000 0.0000; matrix 47; -0.5000 -0.8090 -0.3090 0.0000; 0.8090 -0.3090 -0.5000 0.0000; 0.3090 -0.5000 0.8090 0.0000; matrix 48; 0.3090 -0.5000 0.8090 0.0000; -0.5000 -0.8090 -0.3090 0.0000; 0.8090 -0.3090 -0.5000 0.0000; matrix 49; -0.3090 -0.5000 -0.8090 0.0000; 0.5000 -0.8090 0.3090 0.0000; -0.8090 -0.3090 0.5000 0.0000; matrix 50; -0.8090 -0.3090 0.5000 0.0000; -0.3090 -0.5000 -0.8090 0.0000; 0.5000 -0.8090 0.3090 0.0000; matrix 51; 0.5000 -0.8090 0.3090 0.0000; 0.8090 0.3090 -0.5000 0.0000; 0.3090 0.5000 0.8090 0.0000; matrix 52; 0.3090 0.5000 0.8090 0.0000; 0.5000 -0.8090 0.3090 0.0000; 0.8090 0.3090 -0.5000 0.0000; matrix 53; -0.5000 -0.8090 0.3090 0.0000; 0.8090 -0.3090 0.5000 0.0000; -0.3090 0.5000 0.8090 0.0000; matrix 54; -0.3090 0.5000 0.8090 0.0000; -0.5000 -0.8090 0.3090 0.0000; 0.8090 -0.3090 0.5000 0.0000; matrix 55; -0.8090 -0.3090 -0.5000 0.0000; -0.3090 -0.5000 0.8090 0.0000; -0.5000 0.8090 0.3090 0.0000; matrix 56; -0.5000 0.8090 0.3090 0.0000; -0.8090 -0.3090 -0.5000 0.0000; -0.3090 -0.5000 0.8090 0.0000; matrix 57; 0.0000 0.0000 -1.0000 0.0000; -1.0000 0.0000 0.0000 0.0000; 0.0000 1.0000 0.0000 0.0000; matrix 58; 0.0000 1.0000 0.0000 0.0000; 0.0000 0.0000 -1.0000 0.0000; -1.0000 0.0000 0.0000 0.0000; matrix 59; 0.8090 -0.3090 -0.5000 0.0000; -0.3090 0.5000 -0.8090 0.0000; 0.5000 0.8090 0.3090 0.0000; matrix 60; 0.5000 0.8090 0.3090 0.0000; 0.8090 -0.3090 -0.5000 0.0000; -0.3090 0.5000 -0.8090 0.0000

Sample components

Entire : Sputnik

• Entire: Name: Sputnik

Components

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

Supramolecule #1000: Sputnik

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

Supramolecule #1: Sputnik virophage

• Supramolecule: Name: 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 shell: Shell ID: 1 / Name: gp20 / Diameter: 730 Å / T number (triangulation number): 27

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 1 mg/mL
• Buffer: pH: 7.4 / Details: PBS
• Grid: Details: Holey grids
• Vitrification: Cryogen 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

Electron microscopy

• Microscope: FEI/PHILIPS CM200FEG
• Electron beam: Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Calibrated magnification: 39190 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.582 µm / Nominal defocus min: 0.767 µm / Nominal magnification: 38000
• Sample stage: Specimen holder: Side entry liquid nitrogen-cooled cryo specimen holder; Specimen holder model: GATAN LIQUID NITROGEN
• Image recording: Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 115 / Average electron dose: 20 e/Ų

Image processing

• CTF correction: Details: Each micrograph
• Final reconstruction: Applied 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

Atomic model buiding 1

Initial model

PDB ID:

1m3y
PDB Unreleased entry

• Software: Name: EMFIT
• Details: Protocol: Rigid Body
• Refinement: Space: 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