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- EMDB-68052: Cryo-EM structure of the tail sheath from the contracted phi92 ba... -

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Basic information

Entry
Database: EMDB / ID: EMD-68052
TitleCryo-EM structure of the tail sheath from the contracted phi92 bacteriophage
Map data
Sample
  • Complex: Escherichia phage phi92
    • Protein or peptide: Phi92_gp130
Keywordscontracted sheath / VIRAL PROTEIN
Function / homologyProtein of unknown function DUF3383 / E217 tail sheath protein gp31-like, N-terminal domain / Phi92_gp130
Function and homology information
Biological speciesEscherichia phage phi92 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsChen Y / Liu HR
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32430020 China
National Natural Science Foundation of China (NSFC)32071209 China
CitationJournal: To Be Published
Title: Cryo-EM structure of the tail sheath from the contracted phi92 bacteriophage
Authors: Chen Y / Liu HR
History
DepositionDec 31, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_68052.png

Downloads & links

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Map

FileDownload / File: emd_68052.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 360 pix.
= 504. Å		1.4 Å/pix.
x 360 pix.
= 504. Å		1.4 Å/pix.
x 360 pix.
= 504. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.37
Minimum - Maximum-0.99235725 - 1.5085504
Average (Standard dev.)0.0015305039 (±0.10102885)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 504.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_68052_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_68052_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Escherichia phage phi92

EntireName: Escherichia phage phi92 (virus)
Components
  • Complex: Escherichia phage phi92
    • Protein or peptide: Phi92_gp130

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Supramolecule #1: Escherichia phage phi92

SupramoleculeName: Escherichia phage phi92 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage phi92 (virus)

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Macromolecule #1: Phi92_gp130

MacromoleculeName: Phi92_gp130 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 51.142324 KDa
SequenceString: MATFRDKVVS VTLTYGATSI SETQFDIPLI LTGHNVTGNL VDYFTSSDAL LQAGFGTADP AYKMAKLLFD GLFAPEQVIV GKRDVSKTT LTPVVEDSAT YVITIKANSK SKDFKFVADD TATAQEIVVG LTEMINADVV YKEFFTVSND GSVITVTPVA G KYATMDSS ...String:
MATFRDKVVS VTLTYGATSI SETQFDIPLI LTGHNVTGNL VDYFTSSDAL LQAGFGTADP AYKMAKLLFD GLFAPEQVIV GKRDVSKTT LTPVVEDSAT YVITIKANSK SKDFKFVADD TATAQEIVVG LTEMINADVV YKEFFTVSND GSVITVTPVA G KYATMDSS GFTTKVEYAN DILEDIAKIA DYENSWFWLL SDSHAEQDII DLAGYVEEHD KVYFFSTSQP GVLTKEEDNI LE RLGDMGY NNTCMALWMT NADTVFPEAA VVGSICSATP GTTTLHGKTL VGIEIEKLGQ TAENFIVQQN GNIYRKEHGV LFY RDGFMV SGFYVDYVVH ALWFKARVEE SLFALFKQQS MLGSGVRATS AGLALIRQAV TANPIQVGIN NGSIANEVVT SEET GLLVS LKPTIYIPSR ADMTDAQINA RLVDGMVIEY VYAGFFHYVK VQVNVLTNRT ANSQNSNSST VSS

UniProtKB: Phi92_gp130

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 4500
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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