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- EMDB-62664: Cryo-EM structure of bacteriophage T1 capsid -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-62664
TitleCryo-EM structure of bacteriophage T1 capsid
Map data
Sample
  • Complex: Escherichia phage T1
    • Protein or peptide: Major capsid protein
    • Protein or peptide: cement protein II
    • Protein or peptide: BIG2 domain-containing protein
Keywordscapsid / phage / Viral gene product / VIRAL PROTEIN
Function / homology
Function and homology information


Protein of unknown function DUF2184 / Major capsid protein / : / Structural cement protein (E217 gp24/Pam3 gp6) / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Major capsid protein / BIG2 domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesEscherichia phage T1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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 10, 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_62664.png

Downloads & links

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Map

FileDownload / File: emd_62664.map.gz / Format: CCP4 / Size: 421.9 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 480 pix.
= 652.8 Å		1.36 Å/pix.
x 480 pix.
= 652.8 Å		1.36 Å/pix.
x 480 pix.
= 652.8 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: 4.5
Minimum - Maximum-8.748673999999999 - 21.974495000000001
Average (Standard dev.)-0.0026339262 (±0.8845271)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-240-240-240
Dimensions480480480
Spacing480480480
CellA=B=C: 652.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62664_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_62664_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: Major capsid protein
    • Protein or peptide: cement protein II
    • Protein or peptide: BIG2 domain-containing 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: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 35.329426 KDa
SequenceString: MTTKKFDEAD KSNVEMYLIQ AGVKQDAAAT MGIWTAQELH RIKSQSYEED YPVGSALRVF PVTTELSPTD KTFEYMTFDK VGTAQIIAD YTDDLPLVDA LGTSEFGKVF RLGNAYLISI DEIKAGQATG RPLSTRKASA CQLAHDQLVN RLVFKGSAPH K IVSVFNHP ...String:
MTTKKFDEAD KSNVEMYLIQ AGVKQDAAAT MGIWTAQELH RIKSQSYEED YPVGSALRVF PVTTELSPTD KTFEYMTFDK VGTAQIIAD YTDDLPLVDA LGTSEFGKVF RLGNAYLISI DEIKAGQATG RPLSTRKASA CQLAHDQLVN RLVFKGSAPH K IVSVFNHP NITKITSGKW IDVSTMKPET AEAELTQAIE TIETITRGQH RATNILIPPS MRKVLAIRMP ETTMSYLDYF KS QNSGIEI DSIAELEDID GAGTKGVLVY EKNPMNMSIE IPEAFNMLPA QPKDLHFKVP CTSKCTGLTI YRPMTIVLIT GV

UniProtKB: Major capsid protein

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Macromolecule #2: cement protein II

MacromoleculeName: cement protein II / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 17.022135 KDa
SequenceString:
MAQINASYQR DMAIALPGMV ADTSKYNIDG ACVVNEGDVL VGAAVQVVQA QAVDGHKLVK ALTTGTTPYG VAIRSHWQTV NAQNQMIYE DGGAINVMTS GRVWMLSKST EAPTFGSAVK LDVDGQEKSD GTIETTWTYA GGWTKYKDIQ LVEVQLHQL

UniProtKB: Uncharacterized protein

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Macromolecule #3: BIG2 domain-containing protein

MacromoleculeName: BIG2 domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T1 (virus)
Molecular weightTheoretical: 26.605688 KDa
SequenceString: MAYENLMLRP ACPGNLSDTS TYNIDGACVA QGDIEFGSAV QVVGIVDGVK VVTALSDGGT PYGIAFRSQY EHLSGKILDG EVCNVVSHG RVWALTSLDE APSLFSKLQF GSGGVVTGGS GYAGWTFAGG FVKHEDGYII EVRVKQNAFI VPPPPPPVVL V ESATITTD ...String:
MAYENLMLRP ACPGNLSDTS TYNIDGACVA QGDIEFGSAV QVVGIVDGVK VVTALSDGGT PYGIAFRSQY EHLSGKILDG EVCNVVSHG RVWALTSLDE APSLFSKLQF GSGGVVTGGS GYAGWTFAGG FVKHEDGYII EVRVKQNAFI VPPPPPPVVL V ESATITTD KESPQPNNVT IQCVANALPA NATDKTGKWS IDATNIATVN PDSGLVTPVG GEVVGDFNIT WTANDASKTT AT IAYRVEA VPTPEVDV

UniProtKB: BIG2 domain-containing 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: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 320031
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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