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- EMDB-62699: Structure of flexible tail tube of bacteriophage T1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62699
TitleStructure of flexible tail tube of bacteriophage T1
Map data
Sample
  • Complex: Escherichia phage T1
    • Protein or peptide: Putative major tail protein
Keywordstail tube / phage / VIRUS PROTEIN / VIRAL PROTEIN
Function / homologyPhage tail tube protein 3 / Phage tail tube protein, TTP / Putative major tail protein
Function and homology information
Biological speciesEscherichia phage T1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 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_62699.png

Downloads & links

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Map

FileDownload / File: emd_62699.map.gz / Format: CCP4 / Size: 52.7 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 240 pix.
= 326.4 Å		1.36 Å/pix.
x 240 pix.
= 326.4 Å		1.36 Å/pix.
x 240 pix.
= 326.4 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: 0.015
Minimum - Maximum-0.007396241 - 0.034169815
Average (Standard dev.)0.00010721081 (±0.0029100678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 326.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62699_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_62699_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: Putative major tail 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: Putative major tail protein

MacromoleculeName: Putative major tail protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 24.084053 KDa
SequenceString: MHLPNGAQIF VETSRGVEVE ATAITNAENP VATVASKGDL AKGDYVIVTQ STWAKMVSRV LIVTDAQETS ITLAGIDTSD TLVFPAGGT MSFAKITGWT EIPCVQEIGQ DGGEQQYYTY QCLSDDKEQQ IPTFKSAVSL TYTFAHEFDN PIYPILRKLD S SGQVTAVR ...String:
MHLPNGAQIF VETSRGVEVE ATAITNAENP VATVASKGDL AKGDYVIVTQ STWAKMVSRV LIVTDAQETS ITLAGIDTSD TLVFPAGGT MSFAKITGWT EIPCVQEIGQ DGGEQQYYTY QCLSDDKEQQ IPTFKSAVSL TYTFAHEFDN PIYPILRKLD S SGQVTAVR MYVPKASEMR MWAGILSFND IPSTQVNEME TVELAVSLKG DFTFISSTLA SPGA

UniProtKB: Putative major tail 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: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 34215
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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