+Open data
-Basic information
Entry | Database: PDB / ID: 8ck1 | ||||||
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Title | Carin 1 bacteriophage tail, connector and tail fibers assembly | ||||||
Components |
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Keywords | VIRUS / Bacteriophages / virus structure / Cryo-EM / marine podovirus / tail assembly / connector / tail fibers / depolymerase | ||||||
Biological species | Bacteriophage sp. (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | d'Acapito, A. / Neumann, E. / Schoehn, G. | ||||||
Funding support | France, 1items
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Citation | Journal: J Virol / Year: 2023 Title: Structural Study of the Cobetia marina Bacteriophage 1 (Carin-1) by Cryo-EM. Authors: Alessio d'Acapito / Thomas Roret / Eleftherios Zarkadas / Pierre-Yves Mocaër / Florian Lelchat / Anne-Claire Baudoux / Guy Schoehn / Emmanuelle Neumann / Abstract: Most of studied bacteriophages (phages) are terrestrial viruses. However, marine phages are shown to be highly involved in all levels of oceanic regulation. They are, however, still largely ...Most of studied bacteriophages (phages) are terrestrial viruses. However, marine phages are shown to be highly involved in all levels of oceanic regulation. They are, however, still largely overlooked by the scientific community. By inducing cell lysis on half of the bacterial population daily, their role and influence on the bacterial biomass and evolution, as well as their impact in the global biogeochemical cycles, is undeniable. Cobetia marina (Carin-1) is a member of the family infecting the γ. marina. Here, we present the almost complete, nearly-atomic resolution structure of Carin-1 comprising capsid, portal, and tail machineries at 3.5 Å, 3.8 Å and 3.9 Å, respectively, determined by cryo-electron microscopy (cryo-EM). Our experimental results, combined with AlphaFold2 (AF), allowed us to obtain the nearly-atomic structure of Carin-1 by fitting and refining the AF atomic models in the high resolution cryo-EM map, skipping the bottleneck of manual building and speeding up the structure determination process. Our structural results highlighted the T7-like nature of Carin1, as well as several novel structural features like the presence of short spikes on the capsid, reminiscent those described for Rhodobacter capsulatus gene transfer agent (RcGTA). This is, to our knowledge, the first time such assembly is described for a bacteriophage, shedding light into the common evolution and shared mechanisms between gene transfer agents and phages. This first full structure determined for a marine podophage allowed to propose an infection mechanism different than the one proposed for the archetypal podophage T7. Oceans play a central role in the carbon cycle on Earth and on the climate regulation (half of the planet's CO2 is absorbed by phytoplankton photosynthesis in the oceans and just as much O2 is liberated). The understanding of the biochemical equilibriums of marine biology represents a major goal for our future. By lysing half of the bacterial population every day, marine bacteriophages are key actors of these equilibriums. Despite their importance, these marine phages have, so far, only been studied a little and, in particular, structural insights are currently lacking, even though they are fundamental for the understanding of the molecular mechanisms of their mode of infection. The structures described in our manuscript allow us to propose an infection mechanism that differs from the one proposed for the terrestrial T7 virus, and might also allow us to, in the future, better understand the way bacteriophages shape the global ecosystem. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ck1.cif.gz | 309.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ck1.ent.gz | 236.7 KB | Display | PDB format |
PDBx/mmJSON format | 8ck1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ck1_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8ck1_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8ck1_validation.xml.gz | 60.9 KB | Display | |
Data in CIF | 8ck1_validation.cif.gz | 90.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/8ck1 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/8ck1 | HTTPS FTP |
-Related structure data
Related structure data | 16689MC 8cjzC 8ck0C 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: 91324.289 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacteriophage sp. (virus) / Plasmid details: Cobetia Marina Phage 1 | ||
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#2: Protein | Mass: 86858.156 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bacteriophage sp. (virus) / Plasmid details: Cobetia Marina Phage 1 #3: Protein | Mass: 24697.715 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bacteriophage sp. (virus) / Plasmid details: Cobetia Marina Phage 1 |
-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: Bacteriophage sp. Cobetia Marina Virus Carin1 / Type: VIRUS / Details: Cobetia Marina Virus Carin1 / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Bacteriophage sp. (virus) |
Details of virus | Empty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION |
Natural host | Organism: Cobetia marina / Strain: DSM 4741 |
Buffer solution | pH: 7.5 |
Buffer component | Conc.: 1 x / Name: PBS |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 25mA / Grid material: COPPER/RHODIUM / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 700 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11395 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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