+Open data
-Basic information
Entry | Database: PDB / ID: 7oz4 | ||||||
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Title | Mature capsid of bacteriophage phiRSA1 | ||||||
Components | p2 family phage major capsid protein | ||||||
Keywords | VIRUS / bacteriophage / capsid | ||||||
Function / homology | Bacteriophage P2, capsid / Phage major capsid protein, P2 family / P2 family phage major capsid protein Function and homology information | ||||||
Biological species | Ralstonia virus RSA1 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Effantin, G. / Fujiwara, A. / Kawsaki, T. / Yamada, T. / Schoehn, G. | ||||||
Citation | Journal: Int J Mol Sci / Year: 2021 Title: High Resolution Structure of the Mature Capsid of Bacteriophage ϕRSA1 by Cryo-Electron Microscopy. Authors: Grégory Effantin / Akiko Fujiwara / Takeru Kawasaki / Takashi Yamada / Guy Schoehn / Abstract: The ϕRSA1 bacteriophage has been isolated from , a gram negative bacteria having a significant economic impact on many important crops. We solved the three-dimensional structure of the ϕRSA1 mature ...The ϕRSA1 bacteriophage has been isolated from , a gram negative bacteria having a significant economic impact on many important crops. We solved the three-dimensional structure of the ϕRSA1 mature capsid to 3.9 Å resolution by cryo-electron microscopy. The capsid shell, that contains the 39 kbp of dsDNA genome, has an icosahedral symmetry characterized by an unusual triangulation number of T = 7, . The ϕRSA1 capsid is composed solely of the polymerization of the major capsid protein, gp8, which exhibits the typical "Johnson" fold first characterized in bacteriophage HK97. As opposed to the latter, the ϕRSA1 mature capsid is not stabilized by covalent crosslinking between its subunits, nor by the addition of a decoration protein. We further describe the molecular interactions occurring between the subunits of the ϕRSA1 capsid and their relationships with the other known bacteriophages. | ||||||
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 | 7oz4.cif.gz | 363.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oz4.ent.gz | 303.2 KB | Display | PDB format |
PDBx/mmJSON format | 7oz4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7oz4_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7oz4_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7oz4_validation.xml.gz | 70.2 KB | Display | |
Data in CIF | 7oz4_validation.cif.gz | 105.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oz/7oz4 ftp://data.pdbj.org/pub/pdb/validation_reports/oz/7oz4 | HTTPS FTP |
-Related structure data
Related structure data | 13120MC 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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-Components
#1: Protein | Mass: 37831.531 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Ralstonia virus RSA1 / References: UniProt: A4PE30 |
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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: Ralstonia solanacearum / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Ralstonia solanacearum (bacteria) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION |
Virus shell | Name: gp8 / Diameter: 640 nm / Triangulation number (T number): 7 |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 3399 / Symmetry type: POINT |