25VD | pdb_000025vd

Cap of F2-pyocin

PDB DOI: https://doi.org/10.2210/pdb25VD/pdb
EM Map EMD-80401: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Pseudomonas aeruginosa
Expression System: Pseudomonas aeruginosa
Mutation(s): No

Deposited: 2026-04-19 Released: 2026-08-12
Deposition Author(s): Gu, Z.W., Xie, Y.F., Wang, J.W.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.55 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

F-Type Pyocin Versus Phage lambda Tail: Conserved Hub, Divergent Fibers.

Gu, Z., Xie, Y., Wang, L., Ma, L., Ge, X., Wang, J.

(2026) Adv Sci (Weinh) : e77063-e77063

PubMed: 42573577 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/advs.77063
Primary Citation Related Structures:
25VD, 25VE, 25VF, 25VJ, 26CI

PubMed Abstract:
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.

Organizational Affiliation

State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, P. R. China.

Macromolecule Content

Total Structure Weight: 318.03 kDa
Atom Count: 21,570
Modeled Residue Count: 2,844
Deposited Residue Count: 2,970
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage neck terminator protein gp12-like domain-containing protein	A [auth F] D [auth C] G J M A [auth F], D [auth C], G, J, M, P	167	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: GNQ48_18495
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage tail protein	B [auth A] C [auth B] E [auth D] F [auth E] H B [auth A], C [auth B], E [auth D], F [auth E], H, I, K, L, N, O, Q, R	164	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: VF2, ALP65_01080, DT376_06025, IPC1295_08605
UniProt
Find proteins for Q9R3G3 (Pseudomonas aeruginosa) Explore Q9R3G3 Go to UniProtKB: Q9R3G3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9R3G3
Sequence Annotations Expand
Reference Sequence