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- EMDB-54019: Agrobacterium phage 7-7-1 neck 2 + tail terminator + tail sheath ... -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-54019
TitleAgrobacterium phage 7-7-1 neck 2 + tail terminator + tail sheath + tail tube
Map dataAgrobacterium phage 7-7-1 neck 2 tail terminator sheath tail
Sample
  • Virus: Agrobacterium phage 7-7-1 (virus)
    • Protein or peptide: Structural protein
    • Protein or peptide: Structural protein
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Structural protein
KeywordsFlagella phage / Agrobacterium sp. H13-3 / neck 2 + tail terminator + sheath + tail / VIRUS
Function / homologyBacteriophage SPP1, head-tail adaptor superfamily / Bacteriophage SPP1, head-tail adaptor / Phage head completion protein / Structural protein / Structural protein / Structural protein / Tail sheath protein
Function and homology information
Biological speciesAgrobacterium phage 7-7-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 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_54019.png

Downloads & links

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Map

FileDownload / File: emd_54019.map.gz / Format: CCP4 / Size: 669.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAgrobacterium phage 7-7-1 neck 2 tail terminator sheath tail
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-1.0190579 - 1.8673
Average (Standard dev.)-0.0016700908 (±0.07811914)
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_54019_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 2 tail terminator sheath tail

Fileemd_54019_half_map_1.map
AnnotationAgrobacterium phage 7-7-1 neck 2 tail terminator sheath tail
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 2 tail terminator sheath tail

Fileemd_54019_half_map_2.map
AnnotationAgrobacterium phage 7-7-1 neck 2 tail terminator sheath tail
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
    • Protein or peptide: Structural protein
    • Protein or peptide: Tail sheath protein
    • 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: 6 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 20.292666 KDa
SequenceString:
METKLKLTYS NRLTLPEIAK HIVSPTFHEL EGRAIPVTGV EDDKEGQSAI TKPFALVGLR IGDTSGPAEI GENSRINLRD DFIIEFNFN KDRYKKGGAE TSLFSYYDYE SIRDRLFNAM VAFAGEYGIT FEFVSLDIST EGDTVYIEFR FRQNFDWCEA D RESDTVIK AGSFSLNLKG C

UniProtKB: Structural protein

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Macromolecule #2: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 16.027276 KDa
SequenceString:
MKIKDRKHRV IVCSQKSDVD DNGQLLISRT GSINGWAAIE PVKAIRFSKD GVSMQKDTFQ PTHDITMNYN PDVNISVSAW VYEHRLKSP PRWFKVISVI NVDECSQFMR LRSRLVESND EVEKPVSEEN SFGAVKIDIP L

UniProtKB: Structural protein

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Macromolecule #3: Tail sheath protein

MacromoleculeName: Tail sheath protein / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 54.120355 KDa
SequenceString: MAQDALSDGF VRLCIDPSLN FFGEGCKILV EGQITDDATA AENVVTCVNS ELDLVERFGQ GSVLTESLRK VFCMCKSGVS VYALPRADA AAAVSAVYTL TVTGTALTDG RVQLYMGEAE YSLDIGVDEG DTPTQIAAKI VAAISPDFPY EATAAAGVIT L TARNGGTI ...String:
MAQDALSDGF VRLCIDPSLN FFGEGCKILV EGQITDDATA AENVVTCVNS ELDLVERFGQ GSVLTESLRK VFCMCKSGVS VYALPRADA AAAVSAVYTL TVTGTALTDG RVQLYMGEAE YSLDIGVDEG DTPTQIAAKI VAAISPDFPY EATAAAGVIT L TARNGGTI GNHLSVIYTN LGSCTSVTPE GVTVAFAQTT PGSVNPEPND YASVVNECCF AVYVLSSDDT DWQENLRDWI RS AWDCSKP QCFGHGYVFN KGTLGQVLAD GDNSAELSRL ALPTTYPVLP YLTNAAYGAL SACSTCENPE LNVQGQTYGL LSC INMPES CTPGWEFTEV TQLQNNGFVV SGPATTSGQG NFTSPYIYND VTNYLRDEKN RPNATFRDAS SRRLAAATGV ALAT FLQQF NGLAVFTKNT NIKTGIIGTN LRLMLGKIRK WASDNVGVLF SEFDNINEDI QLVSDFDVQP KCVGQPGVFH LNMRY RPPV RGARINVNLV PALFDNCDR

UniProtKB: Tail sheath protein

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Macromolecule #4: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 4 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Agrobacterium phage 7-7-1 (virus)
Molecular weightTheoretical: 14.503347 KDa
SequenceString:
MACNKQNGVK NILITFTHCD TGEVIGPISH EQPDDTLPTY KTCAWTNTAL TNGAVMRSAS NATMTLPVVR DPRVPLAWYQ GCAQIDAQV EKFDGTVMTL TEGAVTEPEE SDGRAVTMTI IAAEIDELLP PGSLAAA

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: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 4936
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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