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- EMDB-72915: CryoEM structure of F7 pyocin tail fiber in the pre-ejection state -

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Basic information

Entry
Database: EMDB / ID: EMD-72915
TitleCryoEM structure of F7 pyocin tail fiber in the pre-ejection state
Map datastructure of F7 pyocin tail fiber in the pre-ejection state
Sample
  • Complex: F7 pyocin
    • Protein or peptide: Phage tail protein
    • Protein or peptide: Side fiber protein of F7 pyocin
KeywordsPhage / tail / bacteriocin / fibers / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


: / 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
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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_72915.png

Downloads & links

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Map

FileDownload / File: emd_72915.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of F7 pyocin tail fiber in the pre-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: 0.12
Minimum - Maximum-0.27542594 - 0.6994563
Average (Standard dev.)-0.00051569665 (±0.016339812)
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_72915_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_72915_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 A

Fileemd_72915_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: Half Map B

Fileemd_72915_half_map_2.map
AnnotationHalf Map B
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: Side fiber protein of F7 pyocin

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Supramolecule #1: F7 pyocin

SupramoleculeName: F7 pyocin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: 132.953656 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 DNAKIGDEIA SNNYKPDRTG WRLDKNGRFE INGVVEGQGR VTIT NNAIK VFDDKGRLRV HIGDLSA

UniProtKB: Phage tail protein

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Macromolecule #2: Side fiber protein of F7 pyocin

MacromoleculeName: Side fiber protein of F7 pyocin / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 47.743312 KDa
SequenceString: MPWYSTGTVS VVLNSDTVTG SGTAFSANAR AGDAFRGPDG RWYEIGNVSS ATVLTIKPAY QGATANGQAY SITPVQGYSK ALADQLRDL NNQWGSTLAA VKPWATAATG PAALDDMGFG VTGKALAVSA TPVAARSALG VPAVGDYGIG LTAGSSNTLS D ANVVIPNG ...String:
MPWYSTGTVS VVLNSDTVTG SGTAFSANAR AGDAFRGPDG RWYEIGNVSS ATVLTIKPAY QGATANGQAY SITPVQGYSK ALADQLRDL NNQWGSTLAA VKPWATAATG PAALDDMGFG VTGKALAVSA TPVAARSALG VPAVGDYGIG LTAGSSNTLS D ANVVIPNG IYRVASTTAG TMLGSYIGQM LHAEQQGGYG VQLVMAAQTP PQMRMRVKNA GAWQAPVDIL TSNDAANMPL VN LMPDSGR YAGTVNPLAI TLAQPWANST FSSGWNGASF MDGGKFTHDN SSNGGGGAEL NARIQSLLQT MGRSAGGARY GVE FHVAVM TAGIGRANES VGLDGGSRFL AMTNNSRALF CSNQWATVVM WVRVESGSMH IATPAQTTVA VWINGAAKSP GHVL TPAEG WVHVRVATRA WGGYDNAFPY FHTVPGSAVA MACPAWFGGL ADVGIHTAPI ATINGASAA

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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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 359107
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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