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- EMDB-53352: Cryo-tomogram of Agrobacterium phage 7-7-1 and Agrobacterium sp. H13-3 -

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Basic information

Entry
Database: EMDB / ID: EMD-53352
TitleCryo-tomogram of Agrobacterium phage 7-7-1 and Agrobacterium sp. H13-3
Map dataCryo-tomogram of Agrobacterium phage 7-7-1 and Agrobacterium sp. H13-3
Sample
  • Virus: Agrobacterium phage 7-7-1 (virus)
KeywordsFlagella phage / Agrobacterium sp. H13-3 / Capsid / VIRUS
Biological speciesAgrobacterium phage 7-7-1 (virus)
Methodelectron tomography / cryo EM
AuthorsNoteborn WEM / Hoeksma T / Rouchen OY / Briegel A
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
CitationJournal: Commun Biol / Year: 2025
Title: Insights into the structure and initial host attachment of the flagellotropic bacteriophage 7-7-1.
Authors: W E M Noteborn / R Ouyang / T Hoeksma / A Sidi Mabrouk / N C Esteves / D M Pelt / B E Scharf / A Briegel /
Abstract: Understanding the structural and functional mechanisms of bacteriophage 7-7-1, the flagellotropic phage infecting Agrobacterium sp. H13-3, offers promising insights into phage-host interactions. ...Understanding the structural and functional mechanisms of bacteriophage 7-7-1, the flagellotropic phage infecting Agrobacterium sp. H13-3, offers promising insights into phage-host interactions. Using single particle analysis (SPA) cryo-electron microscopy (cryo-EM), we determined the capsid, neck region, tail, and baseplate complex structures. Combined with cryo-electron tomography (cryo-ET) and machine learning methodologies, our findings indicate that phage 7-7-1 uses capsid fibers to establish initial contact with the host flagellum, followed by subsequent attachment to cell surface receptors. The study also demonstrated that capsid fibers are flexible and can interact with other phages and host flagella, suggesting a cooperative infection strategy. These results provide crucial structural insights and may open avenues for developing phage-based therapeutics against resistant bacterial pathogens.
History
DepositionApr 8, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53352.png

Downloads & links

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Map

FileDownload / File: emd_53352.map.gz / Format: CCP4 / Size: 2.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-tomogram of Agrobacterium phage 7-7-1 and Agrobacterium sp. H13-3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.57 Å/pix.
x 320 pix.
= 2103.68 Å		6.57 Å/pix.
x 1573 pix.
= 10340.901 Å		6.57 Å/pix.
x 1230 pix.
= 8086.02 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 6.574 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-19.585882000000002 - 8.167586999999999
Average (Standard dev.)-0.470593 (±0.33008716)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin7492140
Dimensions15731230320
Spacing12301573320
CellA: 8086.02 Å / B: 10340.901 Å / C: 2103.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryo-tomogram of Agrobacterium phage 7-7-1 and Agrobacterium sp....

Fileemd_53352_additional_1.map
AnnotationCryo-tomogram of Agrobacterium phage 7-7-1 and Agrobacterium sp. H13-3
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Agrobacterium phage 7-7-1

EntireName: Agrobacterium phage 7-7-1 (virus)
Components
  • Virus: Agrobacterium phage 7-7-1 (virus)

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Supramolecule #1: Agrobacterium phage 7-7-1

SupramoleculeName: Agrobacterium phage 7-7-1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1161931 / Sci species name: Agrobacterium phage 7-7-1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Agrobacterium sp. H

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aurion / Diameter: 10 nm

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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: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 26000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Number images used: 55
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION

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