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- PDB-25vd: Cap of F2-pyocin -

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Basic information

Entry
Database: PDB / ID: 25vd
TitleCap of F2-pyocin
Components
  • Phage neck terminator protein gp12-like domain-containing protein
  • Phage tail protein
KeywordsVIRAL PROTEIN / pyocin / phage / cap
Function / homologyPhage tail tube protein, lambda-like / Phage tail tube, TTP, lambda-like / : / Phage tail protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsGu, Z.W. / Xie, Y.F. / Wang, J.W.
Funding support China, 1items
OrganizationGrant numberCountry
Other government5262009 China
CitationJournal: Adv Sci (Weinh) / Year: 2026
Title: F-Type Pyocin Versus Phage λ Tail: Conserved Hub, Divergent Fibers.
Authors: Zhiwei Gu / Yufan Xie / Lanxin Wang / Luyan Ma / Xiaofei Ge / Jiawei Wang /
Abstract: Bacteriocins are ribosomally synthesized antimicrobial peptides or proteins that offer an alternative to conventional antibiotics against multidrug-resistant pathogens. Phage tail-like bacteriocins ...Bacteriocins are ribosomally synthesized antimicrobial peptides or proteins that offer an alternative to conventional antibiotics against multidrug-resistant pathogens. Phage tail-like bacteriocins (tailocins) are classified into rigid R-type and flexible F-type variants. While R-type pyocins from Pseudomonas aeruginosa are well-characterized, F-type pyocins remain poorly understood, especially with respect to the molecular mechanisms for their Gram-negative bactericidal activity. Here, we report cryo-electron microscopy structures of the F-type pyocin from P. aeruginosa ATCC 15442 at 2.29-3.26 Å resolution, encompassing three modular components: the tail cap, tail tip, and tail fiber. Structural comparisons with bacteriophage λ reveal a conserved tail tip architecture, including the baseplate hub proteins, distal tail protein, tail assembly protein, and tape measure protein. Unexpectedly, we identify three trimeric side fibers that attach not to the distal tail protein, as in canonical systems, but to the α-helical shaft of the central fiber, indicating a previously unrecognized attachment mode. The receptor-binding domain of the side fiber shares structural similarity with LPS-recognizing domains of R-type pyocins. Together, these results define the structural basis of F-type pyocin assembly and host recognition, reveal conserved and unique features relative to phage λ, and provide a framework for engineering tailocins as precision antimicrobials against drug-resistant P. aeruginosa.
History
DepositionApr 19, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
F: Phage neck terminator protein gp12-like domain-containing protein
A: Phage tail protein
B: Phage tail protein
C: Phage neck terminator protein gp12-like domain-containing protein
D: Phage tail protein
E: Phage tail protein
G: Phage neck terminator protein gp12-like domain-containing protein
H: Phage tail protein
I: Phage tail protein
J: Phage neck terminator protein gp12-like domain-containing protein
K: Phage tail protein
L: Phage tail protein
M: Phage neck terminator protein gp12-like domain-containing protein
N: Phage tail protein
O: Phage tail protein
P: Phage neck terminator protein gp12-like domain-containing protein
Q: Phage tail protein
R: Phage tail protein


Theoretical massNumber of molelcules
Total (without water)318,02618
Polymers318,02618
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Phage neck terminator protein gp12-like domain-containing protein


Mass: 17897.336 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: GNQ48_18495 / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A509JQJ5
#2: Protein
Phage tail protein / VF2 protein


Mass: 17553.525 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: VF2, ALP65_01080, DT376_06025, IPC1295_08605 / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: Q9R3G3
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: F2-pyocin Cap / 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

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 49.91 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27365 / Symmetry type: POINT
RefinementHighest resolution: 2.55 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00222050
ELECTRON MICROSCOPYf_angle_d0.50930042
ELECTRON MICROSCOPYf_dihedral_angle_d4.2423006
ELECTRON MICROSCOPYf_chiral_restr0.0423438
ELECTRON MICROSCOPYf_plane_restr0.0033924

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