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- EMDB-80403: F2-pyocin tail Tip -

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Basic information

Entry
Database: EMDB / ID: EMD-80403
TitleF2-pyocin tail Tip
Map data
Sample
  • Complex: F2-pyocin-tip
    • Protein or peptide: Phage tail protein
    • Protein or peptide: MF2 protein
    • Protein or peptide: F2-pyocin-BHP
    • Protein or peptide: F2-pyocin-tail-fiber
    • Protein or peptide: Lambda phage tail tape-measure protein (Tape_meas_lam_C)
    • Protein or peptide: Putative phage tail assembly protein
  • Ligand: IRON/SULFUR CLUSTER
Keywordstail F2 pyocin tip / VIRAL PROTEIN
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
Phage tail assembly protein / Uncharacterized protein / : / : / Phage tail protein / MF2 protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.29 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_80403.png

Downloads & links

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Map

FileDownload / File: emd_80403.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 480 pix.
= 444.48 Å		0.93 Å/pix.
x 480 pix.
= 444.48 Å		0.93 Å/pix.
x 480 pix.
= 444.48 Å

Surface

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.926 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.88
Minimum - Maximum-2.9443579 - 5.528409
Average (Standard dev.)-0.0012481413 (±0.12802178)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 444.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_80403_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_80403_half_map_2.map
Projections & Slices
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Sample components

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Entire : F2-pyocin-tip

EntireName: F2-pyocin-tip
Components
  • Complex: F2-pyocin-tip
    • Protein or peptide: Phage tail protein
    • Protein or peptide: MF2 protein
    • Protein or peptide: F2-pyocin-BHP
    • Protein or peptide: F2-pyocin-tail-fiber
    • Protein or peptide: Lambda phage tail tape-measure protein (Tape_meas_lam_C)
    • Protein or peptide: Putative phage tail assembly protein
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: F2-pyocin-tip

SupramoleculeName: F2-pyocin-tip / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / 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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Macromolecule #2: MF2 protein

MacromoleculeName: MF2 protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 12.696157 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa (bacteria)
SequenceString:
MADLERFTWD ISIDSAGQAN QLVRQVQYGG GYSQALGDGL NNLSETWQVS RTGDLALIGP IRDFLKRHGG YRSFLWTLPT GEPVRVRAQ GWQLRPRGNG VFTLNTTFQQ VFNP

UniProtKB: MF2 protein

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Macromolecule #3: F2-pyocin-BHP

MacromoleculeName: F2-pyocin-BHP / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 25.248941 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa (bacteria)
SequenceString: MTITADDQAL EPGALVRLFD LDCTGFGGEM LRFHGHLQQG PIHWQGNAYQ AWPLEARGFE QRGDGRASSP TLSVGNIDGS ISALCLFFD GLVGARLTVR ETYAHYLDAA NFAEGNPQAD PSQERLNIWF LEQKTAENSV QVTWELSAPP DFQGQQIPAR Q ITSLCHWC ...String:
MTITADDQAL EPGALVRLFD LDCTGFGGEM LRFHGHLQQG PIHWQGNAYQ AWPLEARGFE QRGDGRASSP TLSVGNIDGS ISALCLFFD GLVGARLTVR ETYAHYLDAA NFAEGNPQAD PSQERLNIWF LEQKTAENSV QVTWELSAPP DFQGQQIPAR Q ITSLCHWC ITNEYRGQDC NYTGTAMFDA DGNPVDDPAL DRCGGRVSDC KLRFGADNPL SHGGFAGAGL VRM

UniProtKB: Uncharacterized protein

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Macromolecule #4: F2-pyocin-tail-fiber

MacromoleculeName: F2-pyocin-tail-fiber / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 130.815414 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa (bacteria)
SequenceString: MNKTITGHKG GSKKPRQPVE MPDSVRSIAR AKILLALGEG EFDGGVDGRS IYLDDTPLLA ADGSVNFPGV TWEFRPGSVD QEHIAGVPA VENELAVGVE LKSDAPWVRA VSNTQLSAVR LRLSWPAIQR QQENGDVVGY RIDYAIDIAV DGGAWQEALK A SLDDKSTS ...String:
MNKTITGHKG GSKKPRQPVE MPDSVRSIAR AKILLALGEG EFDGGVDGRS IYLDDTPLLA ADGSVNFPGV TWEFRPGSVD QEHIAGVPA VENELAVGVE LKSDAPWVRA VSNTQLSAVR LRLSWPAIQR QQENGDVVGY RIDYAIDIAV DGGAWQEALK A SLDDKSTS RYERSHRVDL PEARSGWQVR VRRLTPNQNN NRVADTMRVE AITEVIDAKL RYPNTALLFV EFDASQFQSI PQ ISVEARG RRVRVPSNYD PQTRSYSGTW DGSFKSAWTS NPAWHWYDIV LHKRFGLGRR IDASMVDKWS LYRIAQYCDQ SVP DGKGGQ EPRFSCNLYL QSRAEAWTVL RDLAAIFRGM SYWSGAEMVA VSDMPEDEAY TFSPSNTVRG DDGSHFNYSS SRQR DRHTL ALVNYDNPGN GYQSQPVAVN NDRAQRRYGI SQLEITAIGC TSEGEAQRRG QWALLTEELE QDAVTFRTGM DGRGL APGK IIAVADPVKS GKQIGGRLSA VDGRALTLDR DVEARPGDRL LVNLPNGKAE ARSVQSVVGR VLSVTASYSE TPRPQG QWA LQSNSLTTQR FRIMSITRPE DNLFEITALQ HNASKFDAID NGARIELPPV TSIPPGVQAP PQNVRIKAFT KVDQGLA VT SLSASWDAAP NAVAYEAEWR KDSGNWVRVP RTSALGFDVP GIYAGRYLVR VRALNVMEVG SVYASSEETA LEGKTTPP P ALAYLRCVAG PWRIGLEWGF PASGAADTAY TEIQQSATPG GSEETARALG LFAYPGNTHL VSPIPAGERL AFRGRLIDR SGNVGAWSNW VTGTSSSDAS EYNQLITQEY VESALGQQFF SDIERMQVDI GGLQKQVGDL ADVLLYDPAK VYAKNDMVRQ GQRLYQALK AVPAKTAPPN AAYWSDIGQS LETANGLAQQ VASHTAEISE LDGSLTAQAS RLGVLLAATR DDADDGNGAM A DALRGWKT VARAAQEETV RATENEAQAT RTTLLEARTA DAEGRIATVE RVATSDRQAT AQRLDQLSAS IGGTAASLQS EQ TARANAD SALAQRIDTV QASTDTNSAA IQTTSQAVTS LDGNVKAMYS VKLQAHANGQ KYAAGWQLGF DSGTSVSTMA FQA DRFIWF DSSSGTAVAP VSIVNGQMFI KNALIQDGAI DNAKIGNVIQ SNAMSNNGMP IWRLDKAGTY TVRDSAGQVR VEMG LLQS

UniProtKB: UNIPROTKB: A0A5E5R453

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Macromolecule #5: Lambda phage tail tape-measure protein (Tape_meas_lam_C)

MacromoleculeName: Lambda phage tail tape-measure protein (Tape_meas_lam_C)
type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 63.898121 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa (bacteria)
SequenceString: MATNTDGSLT LDLVLRSEGY RAGMDKVGRI NDQKMRAMEA RAEKAGKAIG KSLDSSALIA SSVLDQALDM LGRTSRQAGQ AKKPVQSAQ DKVLAEWKTR QKELGEAWKS YREPLQDLSK LNEALLKNSS DKLDKALLNL SETGKLSLAN VGKAAYADAA R LASRQMTL ...String:
MATNTDGSLT LDLVLRSEGY RAGMDKVGRI NDQKMRAMEA RAEKAGKAIG KSLDSSALIA SSVLDQALDM LGRTSRQAGQ AKKPVQSAQ DKVLAEWKTR QKELGEAWKS YREPLQDLSK LNEALLKNSS DKLDKALLNL SETGKLSLAN VGKAAYADAA R LASRQMTL MLLDGLFGWV ASVGTEKPKV DDKAGKGQAK AGDDEKEQPS LQSQVFKQWL LQMNSVWGAY RAPLQDISGM TD ELFRNAS EKLEKSLFNF ATTGKLSLSN FAKTVIDDVA RIAARQLSML ALDGLFGWMN GKAGITEAQL ASQKPYTSLL EKA RADAGQ AAAGAPAAQG AAPMPAAAMD VGAMVATASG QTGDGSKVSA GGASASAGKP VGSWVEQMDA SWASLRDQAQ DVSG MMDML FTNAFTNMEN ALFTFATTGK LSFKDFADSV IQDMARIAAR QATLQIIGGI VGAVSGFFGS GATAGSRISD YTGSD MANW VSKQRAGGMP GFARGGAFND GIQSAPALFS MAGGRPALIG ERGPEAIMPL SRGSDGVLGV RALGGGEGGN VFNFST SVS LGGGREGAAT ASGDDGTGQQ LAGMINDAAR NVVAQELRPG GLVWRMVNG

UniProtKB: UNIPROTKB: A0A5D4W7W3

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Macromolecule #6: Putative phage tail assembly protein

MacromoleculeName: Putative phage tail assembly protein / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 21.304693 KDa
Recombinant expressionOrganism: Pseudomonas aeruginosa (bacteria)
SequenceString: MNDTLSQGLT TIRLYGVLGK RFGRMHGRLL ESGTVREAMS ALKHTMEGFE TFMREAESKG LTFAVFRGRT NLSGEQLDMR GREDIRIVP LVIGSKQSGL FQTVLGAALI AVGVFATSLT LGTSTFLISA GASMMLGGVM QMLSPQPKGL KGREAPENAP S YAFGGPVN ...String:
MNDTLSQGLT TIRLYGVLGK RFGRMHGRLL ESGTVREAMS ALKHTMEGFE TFMREAESKG LTFAVFRGRT NLSGEQLDMR GREDIRIVP LVIGSKQSGL FQTVLGAALI AVGVFATSLT LGTSTFLISA GASMMLGGVM QMLSPQPKGL KGREAPENAP S YAFGGPVN TIAQGHPVGV LYGKRRIGGA VISAGIYAED RL

UniProtKB: Phage tail assembly protein

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Macromolecule #7: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 7 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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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: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 93253
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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