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- EMDB-70786: Bacteriophage Ur-lambda TypeIIb infection complex -

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Basic information

Entry
Database: EMDB / ID: EMD-70786
TitleBacteriophage Ur-lambda TypeIIb infection complex
Map dataBacteriophage Ur-lambda TypeIIb infection complex
Sample
  • Virus: Escherichia phage Lambda (virus)
Keywordsbacteriophage / Ur-lambda / infection / VIRAL PROTEIN
Biological speciesEscherichia phage Lambda (virus)
Methodsubtomogram averaging / cryo EM
AuthorsYu H / Liu J / Molineux IJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)124378 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)110243 United States
CitationJournal: Sci Adv / Year: 2025
Title: Structural basis of bacteriophage Ur-lambda infection initiation.
Authors: Huaxin Yu / Chunyan Wang / Jian Yue / Wangbiao Guo / Ian J Molineux / Jun Liu /
Abstract: Bacteriophages must recognize host receptors and penetrate the host cell envelope to initiate infection. How the classic phage λ initiates infection is not yet understood. Here, we combine cryo- ...Bacteriophages must recognize host receptors and penetrate the host cell envelope to initiate infection. How the classic phage λ initiates infection is not yet understood. Here, we combine cryo-electron microscopy and tomography to visualize infection initiation by Ur-λ, the original λ isolate that uses side fibers to adsorb rapidly to . We determine the structure of Ur-λ, resolving the full-length central and side fibers, thus providing a structural basis for host recognition. We show that Ur-λ contains six copies of its tape measure protein. We capture intermediates of the tail tip complex during infection initiation, revealing how extensive conformational changes enable adsorption, and visualize the trans-envelope channel required for genome ejection.
History
DepositionMay 22, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70786.png

Downloads & links

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Map

FileDownload / File: emd_70786.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBacteriophage Ur-lambda TypeIIb infection complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.3 Å/pix.
x 160 pix.
= 687.36 Å		4.3 Å/pix.
x 160 pix.
= 687.36 Å		4.3 Å/pix.
x 160 pix.
= 687.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.296 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.3827531 - 0.3833241
Average (Standard dev.)-0.00026522164 (±0.012213616)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 687.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Bacteriophage Ur-lambda TypeIIb infection complex half map2

Fileemd_70786_half_map_1.map
AnnotationBacteriophage Ur-lambda TypeIIb infection complex half map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Bacteriophage Ur-lambda TypeIIb infection complex half map1

Fileemd_70786_half_map_2.map
AnnotationBacteriophage Ur-lambda TypeIIb infection complex half map1
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 Lambda

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

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Supramolecule #1: Escherichia phage Lambda

SupramoleculeName: Escherichia phage Lambda / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 2681611 / Sci species name: Escherichia phage Lambda / 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
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionSoftware - Name: I3 / Number subtomograms used: 251
ExtractionNumber tomograms: 328 / Number images used: 1556
CTF correctionSoftware - Name: Gctf / Type: NONE

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