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Yorodumi- PDB-3j26: The 3.5 A resolution structure of the Sputnik virophage by cryo-EM -
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-Basic information
Entry | Database: PDB / ID: 3j26 | ||||||
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Title | The 3.5 A resolution structure of the Sputnik virophage by cryo-EM | ||||||
Components |
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Keywords | VIRUS / double jelly-roll / single jelly-roll | ||||||
Function / homology | Jelly Rolls - #1100 / viral capsid / Jelly Rolls / Sandwich / Mainly Beta / Putative capsid protein V20 / Minor virion protein Function and homology information | ||||||
Biological species | Sputnik virophage (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Zhang, X.Z. | ||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3j26.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3j26.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 3j26.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3j26_validation.pdf.gz | 984.9 KB | Display | wwPDB validaton report |
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Full document | 3j26_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 3j26_validation.xml.gz | 255.2 KB | Display | |
Data in CIF | 3j26_validation.cif.gz | 363.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j2/3j26 ftp://data.pdbj.org/pub/pdb/validation_reports/j2/3j26 | HTTPS FTP |
-Related structure data
Related structure data | 5495MC 5496C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 56245.621 Da / Num. of mol.: 13 / Fragment: SEE REMARK 999 / Source method: isolated from a natural source / Source: (natural) Sputnik virophage (virus) / References: UniProt: B4YNG0 #2: Protein | | Mass: 42703.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sputnik virophage (virus) / References: UniProt: I0CES9 Sequence details | FULL-LENGTH CAPSID PROTEIN V20 (MAJOR CAPSID PROTEIN) WAS PRESENT IN THE SAMPLE, BUT ONLY UNP ...FULL-LENGTH CAPSID PROTEIN V20 (MAJOR CAPSID PROTEIN) WAS PRESENT IN THE SAMPLE, BUT ONLY UNP RESIDUES 1-508 WERE MODELED. | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Sputnik virus / Type: VIRUS |
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Details of virus | Empty: NO / Enveloped: NO / Host category: EUKARYOTE / Isolate: STRAIN / Type: SATELLITE |
Natural host | Organism: Acanthamoeba |
Buffer solution | Name: PBS / pH: 7 / Details: PBS |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 400 mesh copper grid with 1.2 um holes |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temp: 100 K / Humidity: 90 % Details: 6 second blot, plunged into liquid ethane (GATAN CRYOPLUNGE 3) Method: 6 second blot |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Jan 1, 2011 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm |
Specimen holder | Temperature: 100 K |
Image recording | Electron dose: 22 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: each particle | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: projection matching / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 12000 / Actual pixel size: 1.1 Å / Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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