+Open data
-Basic information
Entry | Database: PDB / ID: 8a04 | ||||||
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Title | Bacteriophage phiCjT23 major capsid protein trimer type 4 | ||||||
Components | Major capsid protein P5 | ||||||
Keywords | VIRUS / bacteriophage / phiCjT23 | ||||||
Biological species | Flavobacterium phage (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Rissanen, I. / Kejzar, N. / Huiskonen, J.T. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2022 Title: Cryo-EM structure of ssDNA bacteriophage ΦCjT23 provides insight into early virus evolution. Authors: Nejc Kejzar / Elina Laanto / Ilona Rissanen / Vahid Abrishami / Muniyandi Selvaraj / Sylvain Moineau / Janne Ravantti / Lotta-Riina Sundberg / Juha T Huiskonen / Abstract: The origin of viruses remains an open question. While lack of detectable sequence similarity hampers the analysis of distantly related viruses, structural biology investigations of conserved capsid ...The origin of viruses remains an open question. While lack of detectable sequence similarity hampers the analysis of distantly related viruses, structural biology investigations of conserved capsid protein structures facilitate the study of distant evolutionary relationships. Here we characterize the lipid-containing ssDNA temperate bacteriophage ΦCjT23, which infects Flavobacterium sp. (Bacteroidetes). We report ΦCjT23-like sequences in the genome of strains belonging to several Flavobacterium species. The virion structure determined by cryogenic electron microscopy reveals similarities to members of the viral kingdom Bamfordvirae that currently consists solely of dsDNA viruses with a major capsid protein composed of two upright β-sandwiches. The minimalistic structure of ΦCjT23 suggests that this phage serves as a model for the last common ancestor between ssDNA and dsDNA viruses in the Bamfordvirae. Both ΦCjT23 and the related phage FLiP infect Flavobacterium species found in several environments, suggesting that these types of viruses have a global distribution and a shared evolutionary origin. Detailed comparisons to related, more complex viruses not only expand our knowledge about this group of viruses but also provide a rare glimpse into early virus evolution. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a04.cif.gz | 126.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a04.ent.gz | 99.6 KB | Display | PDB format |
PDBx/mmJSON format | 8a04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8a04_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8a04_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8a04_validation.xml.gz | 30.7 KB | Display | |
Data in CIF | 8a04_validation.cif.gz | 45.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/8a04 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/8a04 | HTTPS FTP |
-Related structure data
Related structure data | 15047MC 7zzzC 8a01C 8a02C 8a03C 8a05C 8a06C M: map data used to model this data C: citing same article (ref.) |
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-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 26180.783 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Flavobacterium phage (virus) |
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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: unidentified / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: unidentified (others) |
Details of virus | Empty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Flavobacterium johnsoniae UW101 |
Virus shell | Name: Capsid / Diameter: 600 nm / Triangulation number (T number): 21 |
Buffer solution | pH: 7.2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 300 nm |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 265085 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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