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- EMDB-80401: Cap of F2-pyocin -

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Basic information

Entry
Database: EMDB / ID: EMD-80401
TitleCap of F2-pyocin
Map data
Sample
  • Complex: F2-pyocin Cap
    • Protein or peptide: Phage neck terminator protein gp12-like domain-containing protein
    • Protein or peptide: Phage tail protein
Keywordspyocin / phage / cap / VIRAL PROTEIN
Function / homologyPhage tail tube protein, lambda-like / Phage tail tube, TTP, lambda-like / : / Phage tail protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsGu ZW / Xie YF / Wang JW
Funding support China, 1 items
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, 2026-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_80401.png

Downloads & links

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Map

FileDownload / File: emd_80401.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 384 pix.
= 355.584 Å		0.93 Å/pix.
x 384 pix.
= 355.584 Å		0.93 Å/pix.
x 384 pix.
= 355.584 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.926 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.625
Minimum - Maximum-2.2510815 - 3.9529579
Average (Standard dev.)-0.002195659 (±0.10346173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 355.58398 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_80401_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_80401_half_map_2.map
Projections & Slices
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Sample components

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Entire : F2-pyocin Cap

EntireName: F2-pyocin Cap
Components
  • Complex: F2-pyocin Cap
    • Protein or peptide: Phage neck terminator protein gp12-like domain-containing protein
    • Protein or peptide: Phage tail protein

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Supramolecule #1: F2-pyocin Cap

SupramoleculeName: F2-pyocin Cap / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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

MacromoleculeName: Phage neck terminator protein gp12-like domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 17.897336 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa (bacteria)
SequenceString:
MSSATVRLDH AALRETLRQL FGLPAGSVID ADQLLAPPAI PFMTLRLESS SLLGKVRREF SASGEQESLL ASCESIFRLT WHGPGAHQY LQDACCLLQS GNAGERLRVL KASLLRLTPI ENLSVVQDGQ ALGQARFDLV LAHEHVLLVD LERTASGQAS G GTGGTAY

UniProtKB: UNIPROTKB: A0A509JQJ5

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Macromolecule #2: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 17.553525 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa (bacteria)
SequenceString:
MSILTQGTQI YALVPPVSGT GAATVLEIEG VTSFNPGGNP ADQIEDPCLS DTSRKYKKGL RTPGQATLGI NADPRLASHV RLFQLSEKD GETSVKWAIG WSDGIDVKPT VSTEGDDFVL PPARTWFTFE GYVSDFPFDF ASNTLVATQA TIQRSGAGKW T PKSA

UniProtKB: Phage tail protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.91 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 27365
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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