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- PDB-8env: In situ cryo-EM structure of Pseudomonas phage E217 tail baseplat... -

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Basic information

Entry
Database: PDB / ID: 8env
TitleIn situ cryo-EM structure of Pseudomonas phage E217 tail baseplate in C6 map
Components
  • (Structural protein ...Protein) x 2
  • Baseplate_J domain-containing protein gp44
  • Ripcord gp36
  • Sheath initiator gp34
  • Sheath protein gp31
KeywordsVIRUS / Pseudomonas / phage / baseplate
Function / homology
Function and homology information


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
Baseplate protein J-like domain-containing protein / Tail sheath protein / Putative structural protein / Structural protein / Phage protein / Phage protein
Similarity search - Component
Biological speciesPseudomonas phage vB_PaeM_E217 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å
AuthorsLi, F. / Cingolani, G. / Hou, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)GM140733 United States
CitationJournal: 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
DepositionSep 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sheath protein gp31
B: Sheath protein gp31
C: Sheath protein gp31
D: Sheath protein gp31
E: Sheath protein gp31
F: Sheath protein gp31
G: Structural protein gp33
H: Sheath initiator gp34
I: Ripcord gp36
J: Baseplate_J domain-containing protein gp44
K: Structural protein gp45
L: Structural protein gp33
M: Sheath initiator gp34
N: Ripcord gp36
O: Baseplate_J domain-containing protein gp44
P: Structural protein gp45
Q: Structural protein gp33
R: Sheath initiator gp34
S: Ripcord gp36
T: Baseplate_J domain-containing protein gp44
U: Structural protein gp45
V: Structural protein gp33
W: Sheath initiator gp34
X: Ripcord gp36
Y: Baseplate_J domain-containing protein gp44
Z: Structural protein gp45
a: Structural protein gp33
b: Sheath initiator gp34
c: Ripcord gp36
d: Baseplate_J domain-containing protein gp44
e: Structural protein gp45
f: Structural protein gp33
g: Sheath initiator gp34
h: Ripcord gp36
i: Baseplate_J domain-containing protein gp44
j: Structural protein gp45


Theoretical massNumber of molelcules
Total (without water)1,142,79036
Polymers1,142,79036
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 4 types, 24 molecules ABCDEFHMRWbgINSXchJOTYdi

#1: Protein
Sheath protein gp31


Mass: 53694.750 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8IA62
#3: Protein
Sheath initiator gp34


Mass: 11769.064 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A6G9LIA6
#4: Protein
Ripcord gp36


Mass: 16110.277 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A5C1KAX6
#5: Protein
Baseplate_J domain-containing protein gp44


Mass: 43207.457 Da / Num. of mol.: 6 / Fragment: triplex gp44-confor 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8HLX5

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Structural protein ... , 2 types, 12 molecules GLQVafKPUZej

#2: Protein
Structural protein gp33 / Structure


Mass: 11575.988 Da / Num. of mol.: 6
Fragment: helices bundle (responsible for connecting ripcord)
Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A6G9LFR0
#6: Protein
Structural protein gp45 / Structure


Mass: 54107.535 Da / Num. of mol.: 6 / Fragment: triplex gp45 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A410T8C1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Pseudomonas phage vB_PaeM_E217 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pseudomonas phage vB_PaeM_E217 (virus)
Details of virusEmpty: YES / Enveloped: YES / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: 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 holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2RELION3.1.2image acquisition
4RELION3.1.2CTF correction
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 9300
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9300 / Symmetry type: POINT

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