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- EMDB-72402: In situ structure of F7 pyocin attached to P. aeruginosa outer me... -

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Basic information

Entry
Database: EMDB / ID: EMD-72402
TitleIn situ structure of F7 pyocin attached to P. aeruginosa outer membrane
Map dataIn situ structure of F7 pyocin attached to P. aeruginosa outer membrane.
Sample
  • Complex: F7 pyocin
Keywordspyocin / bacteriocins / tailocins / VIRUS LIKE PARTICLE
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 18.9 Å
AuthorsTachiyama S / Kumar R / Liu J
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The activity of a phage tail-like bactericidal agent is driven by a massive alpha-helix to beta-strand fold switch
Authors: Tachiyama T / Kumar R / Liu J
History
DepositionAug 29, 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_72402.png

Downloads & links

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Map

FileDownload / File: emd_72402.map.gz / Format: CCP4 / Size: 4.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ structure of F7 pyocin attached to P. aeruginosa outer membrane.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.3 Å/pix.
x 180 pix.
= 773.28 Å		4.3 Å/pix.
x 80 pix.
= 343.68 Å		4.3 Å/pix.
x 80 pix.
= 343.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.296 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.4214513 - 0.7723636
Average (Standard dev.)-0.000000000107596 (±0.057723474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions8080180
Spacing8080180
CellA: 343.68 Å / B: 343.68 Å / C: 773.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map of F7 pyocin attached to P. aeruginosa outer membrane.

Fileemd_72402_half_map_1.map
AnnotationHalf map of F7 pyocin attached to P. aeruginosa outer membrane.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of F7 pyocin attached to P. aeruginosa outer membrane.

Fileemd_72402_half_map_2.map
AnnotationHalf map of F7 pyocin attached to P. aeruginosa outer membrane.
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

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Supramolecule #1: F7 pyocin

SupramoleculeName: F7 pyocin / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Pseudomonas aeruginosa PAO1 (bacteria)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.96 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 18.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: I3 / Number subtomograms used: 3324
ExtractionNumber tomograms: 595 / Number images used: 4654 / Software: (Name: IMOD, I3)
CTF correctionType: PHASE FLIPPING ONLY
Final angle assignmentType: OTHER

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