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- EMDB-72921: Asymmetric cryoEM structure of F7 pyocin tail tip in the post-eje... -

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Basic information

Entry
Database: EMDB / ID: EMD-72921
TitleAsymmetric cryoEM structure of F7 pyocin tail tip in the post-ejection state
Map datasymmetric cryoEM structure of F7 pyocin tail tip in the post-ejection state
Sample
  • Complex: F7 pyocin
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Tail hub protein of F7 pyocin
    • Protein or peptide: Tail assembly protein
    • Protein or peptide: MF2 protein
    • Protein or peptide: Phage tail protein
  • Ligand: IRON/SULFUR CLUSTER
KeywordsPhage / tail / bacteriocin / Pseudomonas / cryoEM / tip / fibers / VIRUS LIKE PARTICLE
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 / : / Tip attachment protein J,FNIII-A domain / : / Domain of unknown function DUF1983 ...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
Uncharacterized protein / Tail assembly protein / Phage tail protein / Phage tail protein / MF2 protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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_72921.png

Downloads & links

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Map

FileDownload / File: emd_72921.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsymmetric cryoEM structure of F7 pyocin tail tip in the post-ejection state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. Å		1.1 Å/pix.
x 400 pix.
= 440. 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: 0.13
Minimum - Maximum-0.3079325 - 1.1737128
Average (Standard dev.)-0.0027318618 (±0.027686989)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 440.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72921_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional Map

Fileemd_72921_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_72921_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_72921_half_map_2.map
AnnotationHalf Map A
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 protein
    • Protein or peptide: Tail hub protein of F7 pyocin
    • Protein or peptide: Tail assembly protein
    • Protein or peptide: MF2 protein
    • Protein or peptide: Phage tail protein
  • Ligand: IRON/SULFUR CLUSTER

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Supramolecule #1: F7 pyocin

SupramoleculeName: F7 pyocin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4-#5, #3
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: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 130.341586 KDa
SequenceString: VRSIARAKIL LALGEGEFDG GVDGRSIYLD DTPLLAADGS VNFPGVTWEF RPGSVDQEHI AGVPAVENEL AVGVELKSDA PWVRAVNNT QLSAVRLRLS WPAIQRQQEN GDVVGYRIDY AIDIAVDGGA WQEALKASLD DKSTSRYERS HRVDLPEARS G WQVRVRRL ...String:
VRSIARAKIL LALGEGEFDG GVDGRSIYLD DTPLLAADGS VNFPGVTWEF RPGSVDQEHI AGVPAVENEL AVGVELKSDA PWVRAVNNT QLSAVRLRLS WPAIQRQQEN GDVVGYRIDY AIDIAVDGGA WQEALKASLD DKSTSRYERS HRVDLPEARS G WQVRVRRL TPNQNNNRIA DTMRVEAITE VIDAKLRYPN TALLFVEFDA SQFQSIPQIS VEARGRRVRV PSNYDPQTRS YS GTWDGSF KSAWTSNPAW HWYDIVLHKR FGLGRRIDAS MVDKWSLYRI AQYCDQSVPD GKGGQEPRFS CNLYLQSRAE AWT VLRDLA AIFRGMSYWS GAEMVAVSDM PEDEAYTFSP SNTVRGDDGS HFNYSSSRQR DRHTLALVNY DNPGNGYQSQ PVAV NNDRA QRRYGISQLE ITAIGCTSEG EAQRRGQWAL LTEELEQDAV TFRTGMDGRG LAPGKIIAVA DPVKSGKQIG GRLSA VDGR ALTLDRDVEA RPGDRLLVNL PNGKAEARSV QSVVGRVLSV TAAYSETPRP QGQWALQSNS LTTQRFRIMS ITRPED NLF EITALQHNAS KFDAIDNGAR IELPPVTSIP PGVQAPPQNV RIKAFTKVDQ GLAVTSLSAS WDAAPNAVAY EAEWRKD SG NWVRVPRTSA LGFDVPGIYA GRYLVRVRAL NVMEVGSVYA SSVETALEGK TTPPPALAYL RCVAGPWRIG LEWGFPAS G AADTAYTEIQ QSATPGGSEE TARALGLFAY PGNTHLVSPI PAGERLAFRG RLIDRSGNVG AWSNWVTGTS SSDASEYNQ LITQEYVESA LGQQFFSDIE RMQVDIGGLQ KQVGDLADVL LYDPAKVYAK NDMVRQGQRL YQALKAVPAK TAPPNAAYWS DIGQSLETA NGLAQQVASH TAEISELDGS LTAQASRLGV LQAATRDDAD DGNGAMADAL RGWKTVARAA QEETVRATEN E AQATRTTL LEARTADAEG RIATVERVAT SDRQATAQRL DQLSASIGGT AASLQSEQTA RANADSALAQ RIDTVQASTD TN SAAIQTT SQAVTSLDGN VKAMYSVKLQ AHANGQKYAA GWQLGFDSGT SVSTMAFQAD RFIWFDSSSG TAVAPVSIVN GQM FIKSAL IQDGTIDNAK IGDEIASNNY KPDRTGWRLD KNGRFEINGV VEGQGRVTIT NNAIKVFDDK GRLRVHIGDL SA

UniProtKB: Phage tail protein

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Macromolecule #2: Tail hub protein of F7 pyocin

MacromoleculeName: Tail hub protein of F7 pyocin / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 25.117746 KDa
SequenceString: TITADDQALE PGALVRLFDL DCTGFGGEML RFHGHLQQGP IHWQGNAYQA WPLEARGFEQ RGDGRASSPT LSVGNIDGSI SALCLFFDG LVGARLTVRE TYAHYLDAAN FAEGNPQADP SQERLNIWFL EQKTAENSVQ VTWELSAPPD FQGQQIPARQ I TSLCHWCI ...String:
TITADDQALE PGALVRLFDL DCTGFGGEML RFHGHLQQGP IHWQGNAYQA WPLEARGFEQ RGDGRASSPT LSVGNIDGSI SALCLFFDG LVGARLTVRE TYAHYLDAAN FAEGNPQADP SQERLNIWFL EQKTAENSVQ VTWELSAPPD FQGQQIPARQ I TSLCHWCI TNEYRGQDCN YTGTAMFDAD GNPVDDPALD RCGGRVSDCK LRFGADNPLS HGGFAGAGLV RM

UniProtKB: Uncharacterized protein

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Macromolecule #3: Phage tail protein

MacromoleculeName: Phage tail protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 17.422328 KDa
SequenceString:
SILTQGTQIY ALVPPVSGTG AATVLEIEGV TSFNPGGNPA DQIEDPCLSD TSRKYKKGLR TPGQATLGIN ADPRLASHVR LFQLSEKDG ETSVKWAIGW SDGIDVKPTV STEGDDFVLP PARTWFTFEG YVSDFPFDFA SNTLVATQAT IQRSGAGKWT P KSA

UniProtKB: Phage tail protein

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Macromolecule #4: Tail assembly protein

MacromoleculeName: Tail assembly protein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 4.405006 KDa
SequenceString:
APSYAFGGPV NTIAQGHPVG VLYGKRRIGG AVISAGIYAE DRL

UniProtKB: Tail assembly protein

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Macromolecule #5: MF2 protein

MacromoleculeName: MF2 protein / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 12.493884 KDa
SequenceString:
DLERFTWDIS IDSAGQANQL VRQVQYGGGY SQALGDGLNN LSETWQVSRT GDLALIGPIR DFLKRHGGYR SFLWTLPTGE PVRVRAQGW QLRPRGNGVF TLNTTFQQVF NP

UniProtKB: MF2 protein

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Macromolecule #6: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 6 / 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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52498
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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