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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: To Be Published
Title: Using cryogenic electron micrography methods to gain insight into structure and initial host attachment of the fagellotrophic bacteriophage 7-7-1
Authors: Noteborn WEM / Hoeksma T / Briegel A
History
DepositionJun 14, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing 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
Contrast
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)

Slices (1/2)

Slices (2/3)

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

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_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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