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- EMDB-52521: Agrobacterium phage 7-7-1 tail -

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Basic information

Entry
Database: EMDB / ID: EMD-52521
TitleAgrobacterium phage 7-7-1 tail
Map dataTail of Agrobacterium phage 7-7-1
Sample
  • Virus: Agrobacterium phage 7-7-1 (virus)
    • Protein or peptide: Tail sheath protein
    • Protein or peptide: Structural protein
KeywordsFlagella phage / Agrobacterium sp. H13-3 / Tail / VIRUS
Function / homologyStructural protein / Tail sheath protein
Function and homology information
Biological speciesAgrobacterium phage 7-7-1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
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: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams /
Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
History
DepositionJan 13, 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_52521.png

Downloads & links

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Map

FileDownload / File: emd_52521.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTail of Agrobacterium phage 7-7-1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.37 Å/pix.
x 320 pix.
= 438.4 Å		1.37 Å/pix.
x 320 pix.
= 438.4 Å		1.37 Å/pix.
x 320 pix.
= 438.4 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: 0.46
Minimum - Maximum-2.7437675 - 4.568295
Average (Standard dev.)0.017300306 (±0.22446801)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 438.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Tail of Agrobacterium phage 7-7-1 half map B

Fileemd_52521_half_map_1.map
AnnotationTail of Agrobacterium phage 7-7-1 half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Tail of Agrobacterium phage 7-7-1 half map A

Fileemd_52521_half_map_2.map
AnnotationTail of Agrobacterium phage 7-7-1 half map A
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: 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: Tail sheath protein

MacromoleculeName: Tail sheath protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / 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 #2: Structural protein

MacromoleculeName: Structural protein / type: protein_or_peptide / ID: 2 / Number of copies: 12 / 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
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) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 21858
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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