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- PDB-8frs: Pseudomonas phage E217 5-fold vertex (capsid and decorating proteins) -

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Basic information

Entry
Database: PDB / ID: 8frs
TitlePseudomonas phage E217 5-fold vertex (capsid and decorating proteins)
Components
  • Major structural protein
  • Structural protein gp24
KeywordsVIRUS / Pseudomonas / phage / E217 / capsid / decorating proteins
Function / homology: / Structural cement protein (E217 gp24/Pam3 gp6) / Capsid and scaffold protein / Virion protein
Function and homology information
Biological speciesPseudomonas phage vB_PaeM_E217 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.96 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
DepositionJan 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 26, 2023Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2May 14, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Major structural protein
A: Major structural protein
C: Major structural protein
D: Major structural protein
E: Major structural protein
F: Major structural protein
f: Structural protein gp24
g: Structural protein gp24
h: Structural protein gp24
H: Major structural protein
G: Major structural protein
I: Major structural protein
J: Major structural protein
K: Major structural protein


Theoretical massNumber of molelcules
Total (without water)446,91614
Polymers446,91614
Non-polymers00
Water00
1


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

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Components

#1: Protein
Major structural protein


Mass: 34735.047 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8HL59
#2: Protein Structural protein gp24


Mass: 21610.312 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage vB_PaeM_E217 (virus) / References: UniProt: A0A2K8HLV9
Has protein modificationN

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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
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

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
2RELION3.1.2image acquisition
8PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 9300
3D reconstructionResolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9300 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00232179
ELECTRON MICROSCOPYf_angle_d0.50943829
ELECTRON MICROSCOPYf_dihedral_angle_d4.244415
ELECTRON MICROSCOPYf_chiral_restr0.0434938
ELECTRON MICROSCOPYf_plane_restr0.0045745

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