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- EMDB-68019: Cryo-EM structure of bacteriophage phi92 mature head -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-68019
TitleCryo-EM structure of bacteriophage phi92 mature head
Map data
Sample
  • Complex: Escherichia phage phi92
    • Protein or peptide: Phi92_gp123
    • Protein or peptide: Phi92_gp124
Keywordshead / phage / VIRAL PROTEIN
Function / homology: / Bacteriophage PhiTE minor capsid decoration protein / Major capsid protein GpE / Phage major capsid protein E / viral capsid / Phi92_gp124 / Phi92_gp123
Function and homology information
Biological speciesEscherichia phage phi92 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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: The in stiu structure of the mature head of bacteriophage phi92
Authors: Chen Y / Liu HR
History
DepositionDec 28, 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_68019.png

Downloads & links

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Map

FileDownload / File: emd_68019.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.)
1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å		1.1 Å/pix.
x 360 pix.
= 396. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-1.1473787 - 1.7907243
Average (Standard dev.)-0.0015109174 (±0.07411455)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_68019_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_68019_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_gp123
    • Protein or peptide: Phi92_gp124

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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_gp123

MacromoleculeName: Phi92_gp123 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 13.86871 KDa
SequenceString:
MATGISLSNY RQEFGHLVLG GVFSSDLGHC VREVNLVKTA TMKIGSVLKA DNTEATAAGE AVKVLLWTDA LFGIDDVAVG DTFTAVVGV RDLTLNRYAV YYKSGDLIDD AGVAALETHD LKLTEKVVFT S

UniProtKB: Phi92_gp123

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Macromolecule #2: Phi92_gp124

MacromoleculeName: Phi92_gp124 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage phi92 (virus)
Molecular weightTheoretical: 37.121785 KDa
SequenceString: MPAIILDQVV DFSPMIELQE TPDTLIASLN LFDVQYHATT AIEIGRQKNA DGLIPARERG GERNFLTMDA PSVKVFRIPF FPLDKNIKA QDIQSFRSFA MGGINDNLRT EAEVVNRYMT QILRDVAKTK EKIFAEAVMG RAYNGVGGAA NSAYDWYTEW G ASQKSVSV ...String:
MPAIILDQVV DFSPMIELQE TPDTLIASLN LFDVQYHATT AIEIGRQKNA DGLIPARERG GERNFLTMDA PSVKVFRIPF FPLDKNIKA QDIQSFRSFA MGGINDNLRT EAEVVNRYMT QILRDVAKTK EKIFAEAVMG RAYNGVGGAA NSAYDWYTEW G ASQKSVSV DFSSTTVSPA ATIEQEARAY IIDQKQDGST ATRIVALCSR EFFASLVNSP FVRQAYQYFQ GTPNLLRDRL SG NMDVQVF EWNGVTYIED IHGNIPAGEA FVLPMGIPDM FQAHYAPADT PELANTVARD LYTFMVSEHR TVQLQSEFSL LAV NTRPEL VVKLTTA

UniProtKB: Phi92_gp124

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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: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 118800
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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