[English] 日本語
Yorodumi- PDB-8fvh: Pseudomonas phage E217 neck (portal, head-to-tail connector, coll... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fvh | ||||||
---|---|---|---|---|---|---|---|
Title | Pseudomonas phage E217 neck (portal, head-to-tail connector, collar and gateway proteins) | ||||||
Components |
| ||||||
Keywords | VIRUS / pseudomonas / phage / E217 | ||||||
Function / homology | Function and homology information Protein of unknown function DUF4054 / Inorganic pyrophosphatase domain / Protein of unknown function (DUF4054) / Inorganic Pyrophosphatase / E217 collar protein gp28 / E217 gateway protein gp29 / Protein of unknown function DUF1073 / Anti-CBASS protein Acb1-like Similarity search - Domain/homology | ||||||
Biological species | Pseudomonas phage vB_PaeM_E217 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||
Authors | Li, F. / Cingolani, G. / Hou, C. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Nat Commun / Year: 2023 Title: High-resolution cryo-EM structure of the Pseudomonas bacteriophage E217. Authors: Fenglin Li / Chun-Feng David Hou / Ravi K Lokareddy / Ruoyu Yang / Francesca Forti / Federica Briani / Gino Cingolani / Abstract: E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Here, we describe the structure of the whole E217 virion before and after ...E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Here, we describe the structure of the whole E217 virion before and after DNA ejection at 3.1 Å and 4.5 Å resolution, respectively, determined using cryogenic electron microscopy (cryo-EM). We identify and build de novo structures for 19 unique E217 gene products, resolve the tail genome-ejection machine in both extended and contracted states, and decipher the complete architecture of the baseplate formed by 66 polypeptide chains. We also determine that E217 recognizes the host O-antigen as a receptor, and we resolve the N-terminal portion of the O-antigen-binding tail fiber. We propose that E217 design principles presented in this paper are conserved across PB1-like Myoviridae phages of the Pbunavirus genus that encode a ~1.4 MDa baseplate, dramatically smaller than the coliphage T4. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8fvh.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8fvh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8fvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fvh_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8fvh_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8fvh_validation.xml.gz | 217.1 KB | Display | |
Data in CIF | 8fvh_validation.cif.gz | 328.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/8fvh ftp://data.pdbj.org/pub/pdb/validation_reports/fv/8fvh | HTTPS FTP |
-Related structure data
Related structure data | 29487MC 8envC 8eonC 8frsC 8fuvC 8fvgC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 14234.122 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8I4A6 #2: Protein | Mass: 21057.492 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8HWZ4 #3: Protein | Mass: 16885.285 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8HNR2 #4: Protein | Mass: 48635.984 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8HWX3 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Pseudomonas phage vB_PaeM_E217 / Type: VIRUS / Entity ID: all / Source: NATURAL |
---|---|
Source (natural) | Organism: Pseudomonas phage vB_PaeM_E217 (virus) |
Details of virus | Empty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRION |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: OTHER / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 9300 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9000 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|