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- PDB-8env: In situ cryo-EM structure of Pseudomonas phage E217 tail baseplat... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8env | ||||||
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Title | In situ cryo-EM structure of Pseudomonas phage E217 tail baseplate in C6 map | ||||||
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![]() | VIRUS / Pseudomonas / phage / baseplate | ||||||
Function / homology | ![]() Protein of unknown function DUF2612 / Protein of unknown function (DUF2612) / Protein of unknown function DUF3383 / Protein of unknown function (DUF3383) / Baseplate protein J-like / Baseplate J-like protein Similarity search - Domain/homology | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å | ||||||
![]() | Li, F. / Cingolani, G. / Hou, C. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.7 MB | Display | ![]() |
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PDB format | ![]() | 1.4 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 28280MC ![]() 8eonC ![]() 8frsC ![]() 8fuvC ![]() 8fvgC ![]() 8fvhC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 4 types, 24 molecules ABCDEFHMRWbgINSXchJOTYdi
#1: Protein | Mass: 53694.750 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #3: Protein | Mass: 11769.064 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Protein | Mass: 16110.277 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) ![]() #5: Protein | Mass: 43207.457 Da / Num. of mol.: 6 / Fragment: triplex gp44-confor 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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-Structural protein ... , 2 types, 12 molecules GLQVafKPUZej
#2: Protein | Mass: 11575.988 Da / Num. of mol.: 6 Fragment: helices bundle (responsible for connecting ripcord) Source method: isolated from a natural source / Source: (natural) ![]() #6: Protein | Mass: 54107.535 Da / Num. of mol.: 6 / Fragment: triplex gp45 / Source method: isolated from a natural source / Source: (natural) ![]() |
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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 |
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Sample preparation
Component | Name: Pseudomonas phage vB_PaeM_E217 / Type: VIRUS / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: ![]() |
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 |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
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) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
Particle selection | Num. of particles selected: 9300 | ||||||||||||||||
Symmetry | Point symmetry: C6 (6 fold cyclic) | ||||||||||||||||
3D reconstruction | Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9300 / Symmetry type: POINT |