+Open data
-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 |
| |||||||||
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 Function and homology information | |||||||||
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 ...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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1662.map.gz | 475.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-1662-v30.xml emd-1662.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
Images | 1662.png | 377.8 KB | ||
Others | pdb_fitting_matrix.txt | 6.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1662 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1662 | HTTPS FTP |
-Related structure data
Related structure data | 3kk5MC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-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 |
|
-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/Å2 |
-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 |