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- EMDB-48572: C12 local connector reconstruction of phage JohannRWettstein (Bas63) -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-48572
TitleC12 local connector reconstruction of phage JohannRWettstein (Bas63)
Map data
Sample
  • Virus: JohannRWettstein (Bas63) (virus)
KeywordsConnector / portal / adaptor / phage / bacteriophage / neck / Bas63 / JohannRWettstein / VIRAL PROTEIN
Biological speciesJohannRWettstein (Bas63) (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsHodgkinson-Bean J
Funding support Japan, 2 items
OrganizationGrant numberCountry
Ministry of Agriculture, Forestry and Fisheries (MAFF)GD0696J004 Japan
Japan Society for the Promotion of Science (JSPS)21K20645 Japan
CitationJournal: Sci Adv / Year: 2025
Title: Cryo-EM structure of bacteriophage Bas63 reveals structural conservation and diversity in the genus.
Authors: James Hodgkinson-Bean / Rafael Ayala / Klemens McJarrow-Keller / Léna Cassin / Georgia L Rutter / Alexander J M Crowe / Matthias Wolf / Mihnea Bostina /
Abstract: The BASEL phage collection was developed to provide access to diverse bacteriophages, distinct from model phages. phage JohannRWettstein (Bas63), a myophage in the collection, is a member of the ...The BASEL phage collection was developed to provide access to diverse bacteriophages, distinct from model phages. phage JohannRWettstein (Bas63), a myophage in the collection, is a member of the subfamily Ounavirinae and the genus. Using cryo-electron microscopy, we investigated Bas63's structure to explore its evolutionary relationships and functional adaptations. Our structures reveal a series of gene products: (i) a capsid decorated with β-tulip proteins at three-fold symmetry axes and a Hoc-like protein at hexamer centers, (ii) a conserved connector with an additional 12-fold ring of collar proteins that extend unique whisker proteins that are structurally related to podophage GP4 tail fibers, and (iii) a baseplate with long tail fibers resembling a contracted form of T4's long tail fibers. Sequence conservation analysis of Bas63 structural proteins across ICTV-recognized supports its role as a structural model for evolution. This study advances the mechanistic understanding of phage architecture and reinforces the structural mosaicism of bacteriophages.
History
DepositionJan 9, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48572.png

Downloads & links

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Map

FileDownload / File: emd_48572.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 320 pix.
= 443.84 Å		1.39 Å/pix.
x 320 pix.
= 443.84 Å		1.39 Å/pix.
x 320 pix.
= 443.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.387 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.559
Minimum - Maximum-1.359339 - 2.7688036
Average (Standard dev.)-0.000060593266 (±0.13132855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 443.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48572_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48572_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : JohannRWettstein (Bas63)

EntireName: JohannRWettstein (Bas63) (virus)
Components
  • Virus: JohannRWettstein (Bas63) (virus)

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Supramolecule #1: JohannRWettstein (Bas63)

SupramoleculeName: JohannRWettstein (Bas63) / type: virus / ID: 1 / Parent: 0
Details: Connector structure of phage JohannRWettstein (Bas63)
NCBI-ID: 2852035 / Sci species name: JohannRWettstein (Bas63) / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Escherichia coli (E. coli)

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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
Component:
ConcentrationNameFormula
10.0 mMTris HCL 7.4
10.0 mMmagnesium sulphateMgSO4
0.01 % W/VGelatin

Details: Phage buffer
VitrificationCryogen name: ETHANE-PROPANE
DetailsMature viral particles with packaged genomes

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 49.6 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20386
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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