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- EMDB-62698: Cryo-EM structure of bacteriophage T1 stopper-tail terminator -

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Basic information

Entry
Database: EMDB / ID: EMD-62698
TitleCryo-EM structure of bacteriophage T1 stopper-tail terminator
Map data
Sample
  • Complex: Escherichia phage T1
    • Protein or peptide: Tail protein
    • Protein or peptide: stopper protein
Keywordsstopper / tail terminator / phage / VIRUS PROTEIN / VIRAL PROTEIN
Function / homologyProtein of unknown function DUF4128 / Phage tail terminator protein / Tail protein / Uncharacterized protein
Function and homology information
Biological speciesEscherichia phage T1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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 situ structure of T-series T1 reveals a conserved Lambda-like tail tip
Authors: Chen Y / Liu HR
History
DepositionDec 12, 2024-
Header (metadata) releaseMar 12, 2025-
Map releaseMar 12, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62698.png

Downloads & links

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Map

FileDownload / File: emd_62698.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å		1.36 Å/pix.
x 320 pix.
= 435.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.6
Minimum - Maximum-6.7087345 - 16.058955999999998
Average (Standard dev.)-0.005448394 (±0.72091514)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 435.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62698_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_62698_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 T1

EntireName: Escherichia phage T1 (virus)
Components
  • Complex: Escherichia phage T1
    • Protein or peptide: Tail protein
    • Protein or peptide: stopper protein

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Supramolecule #1: Escherichia phage T1

SupramoleculeName: Escherichia phage T1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage T1 (virus)

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Macromolecule #1: Tail protein

MacromoleculeName: Tail protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 15.191521 KDa
SequenceString:
MHYELSAAAR AAFLSKYRDF PHYMENRNFT PPKDGGMWLR FNYIEGDTLY LSIDRKCKSY IAIVQIGVVF PPGSGVDEAR LKAKEIADF FKDGKMLNVG YIFEGAIVHQ IVKHESGWMI PVRFTVRVDT KET

UniProtKB: Tail protein

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Macromolecule #2: stopper protein

MacromoleculeName: stopper protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 13.831523 KDa
SequenceString:
MNYSQIERMA RKGVAFFTDP SRPMNLIKQG EYGYDENGFE IPPMEQVIPI SGATRRPNAR EIDGETIRAS DILGIFNNDH EINEGDYIE IDGIRHVVVD ARPVQASLEP VAYRPVLRRV SVGG

UniProtKB: Uncharacterized 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: 7.6
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: 4.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23461
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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