+Open data
-Basic information
Entry | Database: PDB / ID: 8rqe | |||||||||
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Title | Composite map of bacteriophage JBD30 capsid - neck complex | |||||||||
Components |
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Keywords | VIRAL PROTEIN / bacteriophage JBD30 / virion / capsid / connector / neck / portal / adaptor / stopper / tail | |||||||||
Function / homology | Function and homology information Protein of unknown function DUF935 / Protein of unknown function UCP028589 / Protein of unknown function (DUF935) / Bacteriophage Mu, Gene product J / Bacteriophage Mu, Gp36 / Bacteriophage Mu, GpT / Mu-like prophage major head subunit gpT Similarity search - Domain/homology | |||||||||
Biological species | Pseudomonas phage JBD30 (virus) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8 Å | |||||||||
Authors | Valentova, L. / Fuzik, T. / Plevka, P. | |||||||||
Funding support | Czech Republic, European Union, 2items
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Citation | Journal: EMBO J / Year: 2024 Title: Structure and replication of Pseudomonas aeruginosa phage JBD30. Authors: Lucie Valentová / Tibor Füzik / Jiří Nováček / Zuzana Hlavenková / Jakub Pospíšil / Pavel Plevka / Abstract: Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection ...Bacteriophages are the most abundant biological entities on Earth, but our understanding of many aspects of their lifecycles is still incomplete. Here, we have structurally analysed the infection cycle of the siphophage Casadabanvirus JBD30. Using its baseplate, JBD30 attaches to Pseudomonas aeruginosa via the bacterial type IV pilus, whose subsequent retraction brings the phage to the bacterial cell surface. Cryo-electron microscopy structures of the baseplate-pilus complex show that the tripod of baseplate receptor-binding proteins attaches to the outer bacterial membrane. The tripod and baseplate then open to release three copies of the tape-measure protein, an event that is followed by DNA ejection. JBD30 major capsid proteins assemble into procapsids, which expand by 7% in diameter upon filling with phage dsDNA. The DNA-filled heads are finally joined with 180-nm-long tails, which bend easily because flexible loops mediate contacts between the successive discs of major tail proteins. It is likely that the structural features and replication mechanisms described here are conserved among siphophages that utilize the type IV pili for initial cell attachment. #1: Journal: Embo J. / Year: 2024 Title: Structure and replication of Pseudomonas aeruginosa phage JBD30 Authors: Valentova, L. / Plevka, P. / Fuzik, T. / Novacek, J. / Pospisil, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8rqe.cif.gz | 28.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8rqe.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8rqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8rqe_validation.pdf.gz | 9.9 MB | Display | wwPDB validaton report |
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Full document | 8rqe_full_validation.pdf.gz | 9.9 MB | Display | |
Data in XML | 8rqe_validation.xml.gz | 3.2 MB | Display | |
Data in CIF | 8rqe_validation.cif.gz | 5 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rq/8rqe ftp://data.pdbj.org/pub/pdb/validation_reports/rq/8rqe | HTTPS FTP |
-Related structure data
Related structure data | 19439MC 8rk3C 8rk4C 8rk5C 8rk6C 8rk7C 8rk8C 8rk9C 8rkaC 8rkbC 8rkcC 8rknC 8rkoC 8rkxC C: citing same article (ref.) M: map data used to model this data |
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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
-Protein , 6 types, 871 molecules aaabacadaeafanaoapaqarasataAaBaCaDaEaFaGaOaPaQaRaSaTaUbcbdbe...
#1: Protein | Mass: 12112.113 Da / Num. of mol.: 420 / Source method: isolated from a natural source / Details: Minor capsid protein gp39 / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P800 #2: Protein | Mass: 33694.980 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Details: major capsid protein gp38 / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P7W9 #3: Protein | Mass: 16990.168 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: stopper protein gp42 / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P7R4 #4: Protein | Mass: 26983.729 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: major tail protein gp44 / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P801 #5: Protein | Mass: 57791.332 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Details: portal protein gp32 / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P7R0 #6: Protein | Mass: 15155.176 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Details: adaptor protein gp41 / Source: (natural) Pseudomonas phage JBD30 (virus) / References: UniProt: L7P846 |
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-Details
Has protein modification | N |
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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: Pseudomonas phage JBD30 / Type: VIRUS Details: Phage JBD30 was propagated in P. aeruginosa strain BAA-28 and purified using CsCl gradient. Entity ID: all / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 20.19 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Pseudomonas phage JBD30 (virus) | ||||||||||||||||||||
Details of virus | Empty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION | ||||||||||||||||||||
Natural host | Organism: Pseudomonas aeruginosa / Strain: BAA-28 | ||||||||||||||||||||
Virus shell | Name: JBD30 capsid / Diameter: 640 nm / Triangulation number (T number): 7 | ||||||||||||||||||||
Buffer solution | pH: 8 / Details: 10 mM MgSO4, 10 mM NaCl, 50 mM Tris pH 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: phage titer 10^11 PFU | ||||||||||||||||||||
Specimen support | Details: Gatan Solarus II / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 5 sec. / Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 11300 |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 25 / Used frames/image: 1-25 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 13129 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2913 / Symmetry type: POINT |