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- EMDB-37518: Tomogram of DT57C bacteriophage (1 of 9) -

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Basic information

Entry
Database: EMDB / ID: EMD-37518
TitleTomogram of DT57C bacteriophage (1 of 9)
Map dataTomogram of DT57C bacteriophages
Sample
  • Virus: Escherichia phage DT57C (virus)
KeywordsT5 / VIRUS / DT57C
Biological speciesEscherichia phage DT57C (virus)
Methodelectron tomography / cryo EM
AuthorsAyala R / Moiseenko AV / Chen TH / Kulikov EE / Golomidova AK / Orekhov PS / Street MA / Sokolova OS / Letarov AV / Wolf M
Funding support Russian Federation, Japan, 4 items
OrganizationGrant numberCountry
Russian Science Foundation21-44-07002 Russian Federation
Japan Society for the Promotion of Science (JSPS)21K20645 Japan
Japan Society for the Promotion of Science (JSPS)20K06581 Japan
Ministry of Agriculture, Forestry and Fisheries (MAFF)20320378 Japan
CitationJournal: Nat Commun / Year: 2023
Title: Nearly complete structure of bacteriophage DT57C reveals architecture of head-to-tail interface and lateral tail fibers.
Authors: Rafael Ayala / Andrey V Moiseenko / Ting-Hua Chen / Eugene E Kulikov / Alla K Golomidova / Philipp S Orekhov / Maya A Street / Olga S Sokolova / Andrey V Letarov / Matthias Wolf /
Abstract: The T5 family of viruses are tailed bacteriophages characterized by a long non-contractile tail. The bacteriophage DT57C is closely related to the paradigmal T5 phage, though it recognizes a ...The T5 family of viruses are tailed bacteriophages characterized by a long non-contractile tail. The bacteriophage DT57C is closely related to the paradigmal T5 phage, though it recognizes a different receptor (BtuB) and features highly divergent lateral tail fibers (LTF). Considerable portions of T5-like phages remain structurally uncharacterized. Here, we present the structure of DT57C determined by cryo-EM, and an atomic model of the virus, which was further explored using all-atom molecular dynamics simulations. The structure revealed a unique way of LTF attachment assisted by a dodecameric collar protein LtfC, and an unusual composition of the phage neck constructed of three protein rings. The tape measure protein (TMP) is organized within the tail tube in a three-stranded parallel α-helical coiled coil which makes direct contact with the genomic DNA. The presence of the C-terminal fragment of the TMP that remains within the tail tip suggests that the tail tip complex returns to its original state after DNA ejection. Our results provide a complete atomic structure of a T5-like phage, provide insights into the process of DNA ejection as well as a structural basis for the design of engineered phages and future mechanistic studies.
History
DepositionSep 22, 2023-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateJan 3, 2024-
Current statusJan 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37518.png

Downloads & links

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Map

FileDownload / File: emd_37518.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram of DT57C bacteriophages
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.8 Å/pix.
x 1024 pix.
= 9011.2 Å		8.8 Å/pix.
x 300 pix.
= 2640. Å		8.8 Å/pix.
x 1024 pix.
= 9011.2 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 8.8 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum0.0 - 10.050817
Average (Standard dev.)0.77952623 (±0.34315827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions30010241024
Spacing10243001024
CellA: 9011.2 Å / B: 2640.0 Å / C: 9011.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Escherichia phage DT57C

EntireName: Escherichia phage DT57C (virus)
Components
  • Virus: Escherichia phage DT57C (virus)

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Supramolecule #1: Escherichia phage DT57C

SupramoleculeName: Escherichia phage DT57C / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 2681606 / Sci species name: Escherichia phage DT57C / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Electron Microscopy Sciences / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 67.0 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionNumber images used: 61

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