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- PDB-25vf: F2-pyocin tail Tip -

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Basic information

Entry
Database: PDB / ID: 25vf
TitleF2-pyocin tail Tip
Components
  • F2-pyocin-BHP
  • F2-pyocin-tail-fiber
  • Lambda phage tail tape-measure protein (Tape_meas_lam_C)
  • MF2 protein
  • Phage tail protein
  • Putative phage tail assembly protein
KeywordsVIRAL PROTEIN / tail F2 pyocin tip
Function / homology
Function and homology information


iron-sulfur cluster binding / host cell cytoplasm / symbiont entry into host cell
Similarity search - Function
Phage tail tube protein, lambda-like / Phage tail tube, TTP, lambda-like / Bacteriophage lambda, Tail tip protein L / Bacteriophage lambda, Tail tip protein M / Phage minor tail protein L / Phage minor tail protein
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Phage tail assembly protein / Uncharacterized protein / : / : / Phage tail protein / MF2 protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.29 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
b: Phage tail protein
2: Phage tail protein
6: MF2 protein
c: MF2 protein
7: F2-pyocin-BHP
A: F2-pyocin-tail-fiber
5: Lambda phage tail tape-measure protein (Tape_meas_lam_C)
9: Putative phage tail assembly protein
B: Phage tail protein
C: Phage tail protein
D: MF2 protein
E: MF2 protein
F: F2-pyocin-BHP
G: F2-pyocin-tail-fiber
H: Lambda phage tail tape-measure protein (Tape_meas_lam_C)
I: Putative phage tail assembly protein
J: Phage tail protein
K: Phage tail protein
L: MF2 protein
M: MF2 protein
N: F2-pyocin-BHP
O: F2-pyocin-tail-fiber
P: Lambda phage tail tape-measure protein (Tape_meas_lam_C)
Q: Putative phage tail assembly protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)906,35527
Polymers905,30024
Non-polymers1,0553
Water00
1


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

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Components

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Protein , 6 types, 24 molecules b2BCJK6cDELM7FNAGO5HP9IQ

#1: Protein
Phage tail protein / VF2 protein


Mass: 17553.525 Da / Num. of mol.: 6
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
#2: Protein
MF2 protein / Phage tail protein


Mass: 12696.157 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: MF2, ALP65_03087, DT376_27610, IPC1295_08585 / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: Q9S561
#3: Protein F2-pyocin-BHP


Mass: 25248.941 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ALP65_03088 / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A3E1N7Q2
#4: Protein F2-pyocin-tail-fiber


Mass: 130815.414 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: TUEID40_04264 / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A5E5R453
#5: Protein Lambda phage tail tape-measure protein (Tape_meas_lam_C)


Mass: 63898.121 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: TUEID40_04259 / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A5D4W7W3
#6: Protein Putative phage tail assembly protein


Mass: 21304.693 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PA14_08280 / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: A0A0H2ZLF4

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Non-polymers , 1 types, 3 molecules

#7: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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-tip / Type: COMPLEX / Entity ID: #1-#6 / 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
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93253 / Symmetry type: POINT

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