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- EMDB-35003: Focused refinement of the TTrP region of the neck of the DT57C ba... -

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Basic information

Entry
Database: EMDB / ID: EMD-35003
TitleFocused refinement of the TTrP region of the neck of the DT57C bacteriophage in the full state
Map dataFocused map for the TTrP portion of the neck of DT57C
Sample
  • Virus: Escherichia phage DT57C (virus)
KeywordsNeck / T5 / TTrP / VIRUS / VIRAL PROTEIN
Biological speciesEscherichia phage DT57C (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsAyala R / Moiseenko AV / 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
DepositionDec 20, 2022-
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_35003.png

Downloads & links

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Map

FileDownload / File: emd_35003.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocused map for the TTrP portion of the neck of DT57C
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 300 pix.
= 420. Å		1.4 Å/pix.
x 300 pix.
= 420. Å		1.4 Å/pix.
x 300 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.036
Minimum - Maximum-0.054464832 - 0.13083541
Average (Standard dev.)0.00019022082 (±0.0031292283)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 420.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_35003_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_35003_half_map_2.map
AnnotationHalf map A
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 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-#3 / 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
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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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

Startup modelType of model: OTHER / Details: Ab initio model generated in cryoSPARC
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 34102
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: cryoSPARC, RELION)

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