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Yorodumi- PDB-8a06: Flavobacterium infecting lipid-containing phage FLiP penton protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a06 | ||||||
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Title | Flavobacterium infecting lipid-containing phage FLiP penton protein | ||||||
Components | Penton protein P12 | ||||||
Keywords | VIRUS / bacteriophage / Flavobacterium / lipid-containing / phage / FLiP / penton protein | ||||||
Function / homology | DUF3168 domain-containing protein Function and homology information | ||||||
Biological species | Flavobacterium phage FLiP (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
Authors | Rissanen, I. / 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. #1: Journal: Proc Natl Acad Sci U S A / Year: 2017 Title: Virus found in a boreal lake links ssDNA and dsDNA viruses. Authors: Laanto, E. / Mantynen, S. / De Colibus, L. / Marjakangas, J. / Gillum, A. / Stuart, D.I. / Ravantti, J.J. / Huiskonen, J.T. / Sundberg, L.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a06.cif.gz | 33.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a06.ent.gz | 23.8 KB | Display | PDB format |
PDBx/mmJSON format | 8a06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/8a06 ftp://data.pdbj.org/pub/pdb/validation_reports/a0/8a06 | HTTPS FTP |
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-Related structure data
Related structure data | 15051MC 7zzzC 8a01C 8a02C 8a03C 8a04C 8a05C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 16851.057 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Flavobacterium phage FLiP (virus) / References: UniProt: A0A222NP85 |
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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: Flavobacterium phage FLiP / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Flavobacterium phage FLiP (virus) |
Details of virus | Empty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION |
Natural host | Organism: Flavobacterium |
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: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm |
Image recording | Electron dose: 22 e/Å2 / Film or detector model: GATAN K2 SUMMIT (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: C5 (5 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28212 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||
Refine LS restraints |
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