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- EMDB-72919: CryoEM structure of F7 pyocin tail tip in the pre-ejection state -

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Basic information

Entry
Database: EMDB / ID: EMD-72919
TitleCryoEM structure of F7 pyocin tail tip in the pre-ejection state
Map datastructure of F7 pyocin tail tip in the pre-ejection state
Sample
  • Complex: F7 pyocin
    • Protein or peptide: Phage tail tape measure protein
    • Protein or peptide: Phage tail protein
    • Protein or peptide: MF2 protein
    • Protein or peptide: Putative phage tail assembly protein
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Tail hub protein of F7 pyocin
  • Ligand: IRON/SULFUR CLUSTER
KeywordsPhage / tail / bacteriocin / Pseudomonas / cryoEM / tip / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


iron-sulfur cluster binding / host cell cytoplasm / symbiont entry into host cell
Similarity search - Function
Bacteriophage tail tape measure, C-terminal / Lambda phage tail tape-measure protein (Tape_meas_lam_C) / 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 / : / Tip attachment protein J,FNIII-A domain ...Bacteriophage tail tape measure, C-terminal / Lambda phage tail tape-measure protein (Tape_meas_lam_C) / 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 / : / Tip attachment protein J,FNIII-A domain / : / Domain of unknown function DUF1983 / Bacteriophage tail tip fiber protein / Tip attachment protein J / Putative phage tail protein / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Phage tail assembly protein / Uncharacterized protein / Phage tail tape measure protein / Phage tail protein / Phage tail protein / MF2 protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsHe Y / Cai XY / Li ASC / Davidson AR / Zhou ZH
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI094386 United States
CitationJournal: To Be Published
Title: Atomic structures and bactericidal actions of a non-contractile tailocin against Pseudomonas aeruginosa
Authors: He Y / Cai XY / Li ASC / Davidson AR / Zhou ZH
History
DepositionSep 28, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72919.png

Downloads & links

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Map

FileDownload / File: emd_72919.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of F7 pyocin tail tip in the pre-ejection state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 450 pix.
= 495. Å		1.1 Å/pix.
x 450 pix.
= 495. Å		1.1 Å/pix.
x 450 pix.
= 495. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.32238007 - 1.3235484
Average (Standard dev.)-0.00019781968 (±0.019853625)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 495.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72919_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpened map

Fileemd_72919_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_72919_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72919_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : F7 pyocin

EntireName: F7 pyocin
Components
  • Complex: F7 pyocin
    • Protein or peptide: Phage tail tape measure protein
    • Protein or peptide: Phage tail protein
    • Protein or peptide: MF2 protein
    • Protein or peptide: Putative phage tail assembly protein
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Tail hub protein of F7 pyocin
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: F7 pyocin

SupramoleculeName: F7 pyocin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)

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Macromolecule #1: Phage tail tape measure protein

MacromoleculeName: Phage tail tape measure protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 63.854113 KDa
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 ATSGKLSLSN FAKTVIDDVA RIAARQLSML ALDGLFGWMN GKAGITEAQL ASQKPYTSLL EKA RAAAGQ AAAGAPAAQG AAPMPAAAMD VGAMVATASG QTGDGSKVSA GGASASAGKP VGSWVEQMDA SWASLRDQAQ DVSG MMEML FTNAFTNMEN ALFTFATTGK LSFKDFADSV IQDMARIAAR QATLQIIGGI VGAVSGFFGS GATAGSRISD YTGSD MANW VSKQRAGGMP GFARGGAFND GIQSAPALFS MAGGRPALIG ERGPEAIMPL SRGSDGVLGV RALGGGEGGN VFNFST SVS LGGGREGAAT ASGDDGTGQQ LAGMINDAAR NVVAQELRPG GLVWRMVNG

UniProtKB: Phage tail tape measure protein

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Macromolecule #2: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 17.553525 KDa
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 #3: MF2 protein

MacromoleculeName: MF2 protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 12.696157 KDa
SequenceString:
MADLERFTWD ISIDSAGQAN QLVRQVQYGG GYSQALGDGL NNLSETWQVS RTGDLALIGP IRDFLKRHGG YRSFLWTLPT GEPVRVRAQ GWQLRPRGNG VFTLNTTFQQ VFNP

UniProtKB: MF2 protein

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Macromolecule #4: Putative phage tail assembly protein

MacromoleculeName: Putative phage tail assembly protein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 21.277668 KDa
SequenceString: MSDTLSQGLT TIRLYGVLGK RFGRMHGRLL ESGTVREAMS ALKHTMEGFE TFMREAESKG LTFAVFRGRT NLSGEQLDMR GREDIRIVP LVIGSKQSGL FQTVLGAALI AVGVFATSLT LGTSTFLISA GASMMLGGVM QMLSPQPKGL KGREAPENAP S YAFGGPVN ...String:
MSDTLSQGLT 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 #5: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 126.233258 KDa
SequenceString: MNKTITGHKG GSKKPRQPVE MPDSVRSIAR AKILLALGEG EFDGGVDGRS IYLDDTPLLA ADGSVNFPGV TWEFRPGSVD QEHIAGVPA VENELAVGVE LKSDAPWVRA VNNTQLSAVR LRLSWPAIQR QQENGDVVGY RIDYAIDIAV DGGAWQEALK A SLDDKSTS ...String:
MNKTITGHKG GSKKPRQPVE MPDSVRSIAR AKILLALGEG EFDGGVDGRS IYLDDTPLLA ADGSVNFPGV TWEFRPGSVD QEHIAGVPA VENELAVGVE LKSDAPWVRA VNNTQLSAVR LRLSWPAIQR QQENGDVVGY RIDYAIDIAV DGGAWQEALK A SLDDKSTS RYERSHRVDL PEARSGWQVR VRRLTPNQNN NRIADTMRVE 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 VLSVTAAYSE TPRPQG QWA LQSNSLTTQR FRIMSITRPE DNLFEITALQ HNASKFDAID NGARIELPPV TSIPPGVQAP PQNVRIKAFT KVDQGLA VT SLSASWDAAP NAVAYEAEWR KDSGNWVRVP RTSALGFDVP GIYAGRYLVR VRALNVMEVG SVYASSVETA LEGKTTPP P ALAYLRCVAG PWRIGLEWGF PASGAADTAY TEIQQSATPG GSEETARALG LFAYPGNTHL VSPIPAGERL AFRGRLIDR SGNVGAWSNW VTGTSSSDAS EYNQLITQEY VESALGQQFF SDIERMQVDI GGLQKQVGDL ADVLLYDPAK VYAKNDMVRQ GQRLYQALK AVPAKTAPPN AAYWSDIGQS LETANGLAQQ VASHTAEISE LDGSLTAQAS RLGVLQAATR DDADDGNGAM A DALRGWKT VARAAQEETV RATENEAQAT RTTLLEARTA DAEGRIATVE RVATSDRQAT AQRLDQLSAS IGGTAASLQS EQ TARANAD SALAQRIDTV QASTDTNSAA IQTTSQAVTS LDGNVKAMYS VKLQAHANGQ KYAAGWQLGF DSGTSVSTMA FQA DRFIWF DSSSGTAVAP VSIVNGQMFI KSALIQDGTI DNAKIG

UniProtKB: Phage tail protein

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Macromolecule #6: Tail hub protein of F7 pyocin

MacromoleculeName: Tail hub protein of F7 pyocin / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 25.248941 KDa
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 #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-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112611
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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