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- PDB-8eon: Pseudomonas phage E217 baseplate complex -

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Basic information

Entry
Database: PDB / ID: 8eon
TitlePseudomonas phage E217 baseplate complex
Components
  • (Baseplate component ...Tripod (photography)) x 5
  • Baseplate hub gp41
  • Baseplate spike gp43
  • Triplex gp44-b
  • Triplex gp45
KeywordsVIRUS / Pseudomonas / phage / baseplate
Function / homology
Function and homology information


Protein of unknown function DUF2612 / Protein of unknown function (DUF2612) / Phage protein Gp138 N-terminal domain / Phage protein Gp138 N-terminal domain / Phage spike trimer / Phage spike trimer / Baseplate protein J-like / Baseplate J-like protein / Vgr protein, OB-fold domain superfamily
Similarity search - Domain/homology
Baseplate protein J-like domain-containing protein / Phage protein / Tail fiber protein / Phage protein / Baseplate 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: 3.6 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
DepositionOct 3, 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
G: Baseplate component gp33
H: Baseplate component gp34
I: Baseplate component gp36
J: Triplex gp44-b
K: Triplex gp45
L: Baseplate component gp33
M: Baseplate component gp34
N: Baseplate component gp36
O: Triplex gp44-b
P: Triplex gp45
Q: Baseplate component gp33
R: Baseplate component gp34
S: Baseplate component gp36
T: Triplex gp44-b
U: Triplex gp45
V: Baseplate component gp33
W: Baseplate component gp34
X: Baseplate component gp36
Y: Triplex gp44-b
Z: Triplex gp45
a: Baseplate component gp33
b: Baseplate component gp34
c: Baseplate component gp36
d: Triplex gp44-b
e: Triplex gp45
f: Baseplate component gp33
g: Baseplate component gp34
h: Baseplate component gp36
i: Triplex gp44-b
j: Triplex gp45
A: Baseplate component gp37
B: Baseplate component gp37
C: Baseplate component gp37
D: Baseplate component gp38
E: Baseplate hub gp41
F: Baseplate spike gp43
k: Baseplate component gp38
l: Baseplate hub gp41
m: Baseplate hub gp41
n: Baseplate spike gp43
o: Baseplate component gp38
p: Baseplate spike gp43
q: Triplex gp44-b
r: Triplex gp44-b
s: Triplex gp44-b
t: Triplex gp44-b
u: Triplex gp44-b
v: Triplex gp44-b


Theoretical massNumber of molelcules
Total (without water)1,370,00948
Polymers1,370,00948
Non-polymers00
Water0
1


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

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Components

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Baseplate component ... , 5 types, 24 molecules GLQVafHMRWbgINSXchABCDko

#1: Protein
Baseplate component gp33 / Tripod (photography)


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
#2: Protein
Baseplate component gp34 / Tripod (photography)


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
#3: Protein
Baseplate component gp36 / Tripod (photography)


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
#6: Protein Baseplate component gp37 / Tripod (photography)


Mass: 19081.869 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8HNS1
#7: Protein Baseplate component gp38 / Tripod (photography)


Mass: 21169.109 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8I4C0

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Protein , 4 types, 24 molecules JOTYdiqrstuvKPUZejElmFnp

#4: Protein
Triplex gp44-b


Mass: 43207.457 Da / Num. of mol.: 12 / Fragment: triplex gp44-confor 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8HLX5
#5: Protein
Triplex gp45


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
#8: Protein Baseplate hub gp41


Mass: 32480.277 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8IA76
#9: Protein Baseplate spike gp43


Mass: 23982.912 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8ICH7

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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: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 1.25 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 10000 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00997614
ELECTRON MICROSCOPYf_angle_d0.715133089
ELECTRON MICROSCOPYf_dihedral_angle_d6.1213644
ELECTRON MICROSCOPYf_chiral_restr0.04915345
ELECTRON MICROSCOPYf_plane_restr0.00617451

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