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- EMDB-60689: Structure of urea-treated empty bacteriophage T5 connector complex -

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Basic information

Entry
Database: EMDB / ID: EMD-60689
TitleStructure of urea-treated empty bacteriophage T5 connector complex
Map data
Sample
  • Virus: Escherichia phage T5 (virus)
    • Protein or peptide: Tail tube terminator protein p142
KeywordsComplex / VIRAL PROTEIN
Function / homologysymbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / virus tail / Tail tube terminator protein p142
Function and homology information
Biological speciesEscherichia phage T5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsPeng YN / Liu HR
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)31971122 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: Int J Mol Sci / Year: 2024
Title: Structures of Mature and Urea-Treated Empty Bacteriophage T5: Insights into Siphophage Infection and DNA Ejection.
Authors: Yuning Peng / Huanrong Tang / Hao Xiao / Wenyuan Chen / Jingdong Song / Jing Zheng / Hongrong Liu /
Abstract: T5 is a siphophage that has been extensively studied by structural and biochemical methods. However, the complete in situ structures of T5 before and after DNA ejection remain unknown. In this study, ...T5 is a siphophage that has been extensively studied by structural and biochemical methods. However, the complete in situ structures of T5 before and after DNA ejection remain unknown. In this study, we used cryo-electron microscopy (cryo-EM) to determine the structures of mature T5 (a laboratory-adapted, fiberless T5 mutant) and urea-treated empty T5 (lacking the tip complex) at near-atomic resolutions. Atomic models of the head, connector complex, tail tube, and tail tip were built for mature T5, and atomic models of the connector complex, comprising the portal protein pb7, adaptor protein p144, and tail terminator protein p142, were built for urea-treated empty T5. Our findings revealed that the aforementioned proteins did not undergo global conformational changes before and after DNA ejection, indicating that these structural features were conserved among most myophages and siphophages. The present study elucidates the underlying mechanisms of siphophage infection and DNA ejection.
History
DepositionJul 3, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_60689.png

Downloads & links

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Map

FileDownload / File: emd_60689.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 320 pix.
= 416. Å		1.3 Å/pix.
x 320 pix.
= 416. Å		1.3 Å/pix.
x 320 pix.
= 416. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.0
Minimum - Maximum-12.456486 - 18.311125000000001
Average (Standard dev.)0.0033813573 (±0.85502034)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 416.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60689_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_60689_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Escherichia phage T5

EntireName: Escherichia phage T5 (virus)
Components
  • Virus: Escherichia phage T5 (virus)
    • Protein or peptide: Tail tube terminator protein p142

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Supramolecule #1: Escherichia phage T5

SupramoleculeName: Escherichia phage T5 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2695836 / Sci species name: Escherichia phage T5 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Tail tube terminator protein p142

MacromoleculeName: Tail tube terminator protein p142 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T5 (virus)
Molecular weightTheoretical: 18.378643 KDa
SequenceString:
MDHRTSIAQA MVDRISKQMD GSQPDEYFNN LYGNVSRQTY KFEEIREFPY VAVHIGTETG QYLPSGQQWM FLELPILVYD KEKTDIQEQ LEKLVADIKT VIDTGGNLEY TVSKPNGSTF PCEATDMIIT SVSTDEGLLA PYGLAEINVT VRYQPPRRSL R R

UniProtKB: Tail tube terminator protein p142

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN 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: 1.6 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: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 76271
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE

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