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- PDB-9yg8: CryoEM structure of F7 pyocin tail fiber in the pre-ejection state -

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Basic information

Entry
Database: PDB / ID: 9yg8
TitleCryoEM structure of F7 pyocin tail fiber in the pre-ejection state
Components
  • Phage tail protein
  • Side fiber protein of F7 pyocin
KeywordsVIRUS LIKE PARTICLE / Phage / tail / bacteriocin / fibers
Function / homology
Function and homology information


: / Tip attachment protein J,FNIII-A domain / : / Domain of unknown function DUF1983 / Bacteriophage tail tip fiber protein / Tip attachment protein J / Putative phage tail protein / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHe, Y. / Cai, X.Y. / Li, A.S.C. / Davidson, A.R. / Zhou, Z.H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI094386 United States
CitationJournal: To Be Published
Title: Atomic structures and bactericidal actions of a non-contractile tailocin against Pseudomonas aeruginosa
Authors: He, Y. / Cai, X.Y. / Li, A.S.C. / Davidson, A.R. / Zhou, Z.H.
History
DepositionSep 28, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phage tail protein
B: Side fiber protein of F7 pyocin
C: Side fiber protein of F7 pyocin
D: Side fiber protein of F7 pyocin
E: Phage tail protein
F: Side fiber protein of F7 pyocin
G: Side fiber protein of F7 pyocin
H: Side fiber protein of F7 pyocin
I: Phage tail protein
J: Side fiber protein of F7 pyocin
K: Side fiber protein of F7 pyocin
L: Side fiber protein of F7 pyocin


Theoretical massNumber of molelcules
Total (without water)828,55112
Polymers828,55112
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Phage tail protein


Mass: 132953.656 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A7M2ZXW7
#2: Protein
Side fiber protein of F7 pyocin


Mass: 47743.312 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria)
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: F7 pyocin / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 359107 / Symmetry type: POINT
RefinementHighest resolution: 3.1 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00334401
ELECTRON MICROSCOPYf_angle_d0.48746998
ELECTRON MICROSCOPYf_dihedral_angle_d3.7934962
ELECTRON MICROSCOPYf_chiral_restr0.0435316
ELECTRON MICROSCOPYf_plane_restr0.0056189

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