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 25VD | pdb_000025vd

Cap of F2-pyocin


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 25VD

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

  • 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

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phage neck terminator protein gp12-like domain-containing protein167Pseudomonas aeruginosaMutation(s): 0 
Gene Names: GNQ48_18495
UniProt
Find proteins for Q9I547 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I547 
Go to UniProtKB:  Q9I547
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I547
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Phage tail protein164Pseudomonas aeruginosaMutation(s): 0 
Gene Names: VF2, ALP65_01080, DT376_06025, IPC1295_08605
UniProt
Find proteins for G3XD38 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore G3XD38 
Go to UniProtKB:  G3XD38
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG3XD38
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChina5262009

Revision History  (Full details and data files)

  • Version 1.0: 2026-08-12
    Type: Initial release
  • Version 1.1: 2026-08-19
    Changes: Data collection, Database references