+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5496 | |||||||||
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Title | Cryo-EM reconstruction of Sputnik empty virus | |||||||||
Map data | Reconstruction of Sputnik empty particles | |||||||||
Sample |
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Keywords | Jelly roll structure / major capsid protein / penton protein | |||||||||
Biological species | Sputnik virophage (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Zhang XZ / Sun SY / Xiang Y / Wong J / Klose T / Raoult D / Rossmann MG | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_5496.map.gz | 238.7 MB | EMDB map data format | |
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Header (meta data) | emd-5496-v30.xml emd-5496.xml | 9.3 KB 9.3 KB | Display Display | EMDB header |
Images | emd_5496_1.jpg | 235.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5496 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5496 | HTTPS FTP |
-Validation report
Summary document | emd_5496_validation.pdf.gz | 79.6 KB | Display | EMDB validaton report |
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Full document | emd_5496_full_validation.pdf.gz | 78.7 KB | Display | |
Data in XML | emd_5496_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5496 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5496 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5496.map.gz / Format: CCP4 / Size: 843.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of Sputnik empty particles | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Sputnik empty particle
Entire | Name: Sputnik empty particle |
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Components |
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-Supramolecule #1000: Sputnik empty particle
Supramolecule | Name: Sputnik empty particle / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Sputnik virophage
Supramolecule | Name: Sputnik virophage / type: virus / ID: 1 / Details: Sputnik virus empty particle / NCBI-ID: 543939 / Sci species name: Sputnik virophage / Database: NCBI / Virus type: SATELLITE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Acanthamoeba (eukaryote) / synonym: PROTOZOA |
Virus shell | Shell ID: 1 / Name: Vp20 / Diameter: 750 Å / T number (triangulation number): 27 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7 / Details: PBS |
Grid | Details: 400 mesh Cu grid (c-flat), 1.2 um hole, glow discharged, 3nm carbon films |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 100 K / Instrument: GATAN CRYOPLUNGE 3 / Method: blot 6 seconds |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: corrected at 250,000 magnification |
Date | Jan 1, 2011 |
Image recording | Category: 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | Using EMAN |
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CTF correction | Details: each particle |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN, Frealign / Number images used: 12000 |
Final angle assignment | Details: EMAN |