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Yorodumi- PDB-3kk5: Crystal structure of PBCV-1 VP54 fitted into a cryo-EM reconstruc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kk5 | ||||||
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Title | Crystal structure of PBCV-1 VP54 fitted into a cryo-EM reconstruction of the virophage Sputnik | ||||||
Components | Major capsid protein | ||||||
Keywords | VIRUS / double jellyroll / Capsid protein / Late protein / Virion / Icosahedral virus | ||||||
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 | Acanthamoeba polyphaga (eukaryote) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10.6 Å | ||||||
Authors | Sun, S. / Rossmann, M.G. | ||||||
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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3kk5.cif.gz | 168.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kk5.ent.gz | 117.8 KB | Display | PDB format |
PDBx/mmJSON format | 3kk5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kk5_validation.pdf.gz | 964.7 KB | Display | wwPDB validaton report |
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Full document | 3kk5_full_validation.pdf.gz | 964.2 KB | Display | |
Data in XML | 3kk5_validation.xml.gz | 62.7 KB | Display | |
Data in CIF | 3kk5_validation.cif.gz | 96.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kk/3kk5 ftp://data.pdbj.org/pub/pdb/validation_reports/kk/3kk5 | HTTPS FTP |
-Related structure data
Related structure data | 1662MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 48199.625 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Source: (natural) Acanthamoeba polyphaga (eukaryote) / References: UniProt: P30328 |
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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: major capsid protein of sputnik |
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Details of virus | Host category: PROTOZOA / Isolate: SPECIES / Type: SATELLITE |
Natural host | Organism: Acanthamoeba polyphaga |
Buffer solution | Name: PBS / pH: 7.4 / Details: PBS |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: flash-frozen on holey grids in liquid ethane |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM200FEG |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 38000 X / Calibrated magnification: 39190 X / Nominal defocus max: 3582 nm / Nominal defocus min: 767 nm / Cs: 2 mm |
Specimen holder | Temperature: 70 K |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: GENERIC 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: CTF parameters were calculated for particles in each micrograph. | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: projection matching / Resolution: 10.6 Å / Num. of particles: 6780 / Nominal pixel size: 1.62 Å / Actual pixel size: 1.62 Å / Details: EMAN / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Sumf / Details: REFINEMENT PROTOCOL--rigid body | ||||||||||||
Atomic model building | PDB-ID: 1M3Y 1m3y Accession code: 1M3Y / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
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