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- EMDB-54018: Agrobacterium phage 7-7-1 neck 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-54018
TitleAgrobacterium phage 7-7-1 neck 1
Map dataAgrobacterium phage 7-7-1 neck 1
Sample
  • Virus: Agrobacterium phage 7-7-1 (virus)
    • Protein or peptide: Structural protein
KeywordsFlagella phage / Agrobacterium sp. H13-3 / Neck 1 / VIRUS
Function / homologyStructural protein
Function and homology information
Biological speciesAgrobacterium phage 7-7-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsNoteborn WEM / Hoeksma T / 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
DepositionJun 14, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54018.png

Downloads & links

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Map

FileDownload / File: emd_54018.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAgrobacterium phage 7-7-1 neck 1
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 560 pix.
= 767.2 Å		1.37 Å/pix.
x 560 pix.
= 767.2 Å		1.37 Å/pix.
x 560 pix.
= 767.2 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.37 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.318339 - 1.979622
Average (Standard dev.)-0.0020044213 (±0.08879913)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions560560560
Spacing560560560
CellA=B=C: 767.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54018_msk_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Agrobacterium phage 7-7-1 neck 1

Fileemd_54018_half_map_1.map
AnnotationAgrobacterium phage 7-7-1 neck 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Agrobacterium phage 7-7-1 neck 1

Fileemd_54018_half_map_2.map
AnnotationAgrobacterium phage 7-7-1 neck 1
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)
    • Protein or peptide: Structural protein

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Supramolecule #1: Agrobacterium phage 7-7-1

SupramoleculeName: Agrobacterium phage 7-7-1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1161931 / Sci species name: Agrobacterium phage 7-7-1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 22.081221 KDa
SequenceString: MNYETLLPLQ TIREHAKCDD NPRVTDTLLS LYREAAFEAA ELYTGMSFTP QKTIVEPVRI KNRKGKIVLS QVPIAGRPVV FTGGGLGSP LELIPFPNSN VLHFPNGSPD RFQTWGDCHT CGVPSQLMAT YVAGRRCESS VPAGIIMGVL KLIAWNINNP G DEIMSVRN ...String:
MNYETLLPLQ TIREHAKCDD NPRVTDTLLS LYREAAFEAA ELYTGMSFTP QKTIVEPVRI KNRKGKIVLS QVPIAGRPVV FTGGGLGSP LELIPFPNSN VLHFPNGSPD RFQTWGDCHT CGVPSQLMAT YVAGRRCESS VPAGIIMGVL KLIAWNINNP G DEIMSVRN TSTANAQGLI GGTNNGAVVS GAQDEWFRYR RVIL

UniProtKB: Structural protein

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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: 7.4
GridModel: Quantifoil R2/2 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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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: 40.0 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: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 5578
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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