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- EMDB-48256: In situ cryo-EM structure of bacteriophage Ur-lambda tail side fiber -

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Basic information

Entry
Database: EMDB / ID: EMD-48256
TitleIn situ cryo-EM structure of bacteriophage Ur-lambda tail side fiber
Map dataIn situ cryoEM structure of bacteriophage Ur-lambda tail side fiber
Sample
  • Virus: Escherichia phage Ur-lambda (virus)
    • Protein or peptide: Tail fiber protein
Keywordsbacteriophage / tail tip complex / VIRAL PROTEIN
Function / homology
Function and homology information


virus tail, fiber / adhesion receptor-mediated virion attachment to host cell / receptor-mediated virion attachment to host cell / symbiont entry into host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Lambda-like tail fibre protein, N-terminal / Prophage tail fibre N-terminal / Bacteriophage lambda, Tail fiber protein, repeat-1 / Phage tail fibre repeat / Bacteriophage lambda, Tail fiber protein, repeat-2 / Phage tail fibre repeat / Phage tail collar domain superfamily / Phage tail collar domain / : / Phage Tail Collar Domain / Carboxypeptidase-like, regulatory domain superfamily
Similarity search - Domain/homology
Biological speciesEscherichia phage Lambda (virus) / Escherichia phage Ur-lambda (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
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
DepositionDec 10, 2024-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48256.png

Downloads & links

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Map

FileDownload / File: emd_48256.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIn situ cryoEM structure of bacteriophage Ur-lambda tail side fiber
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 131 pix.
= 143.838 Å		1.1 Å/pix.
x 131 pix.
= 143.838 Å		1.1 Å/pix.
x 42 pix.
= 46.116 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.098 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.4234489 - 0.72316015
Average (Standard dev.)0.019098775 (±0.08030312)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin16091160
Dimensions13142131
Spacing13113142
CellA: 143.83801 Å / B: 143.83801 Å / C: 46.116 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Bacteriophage Ur-lambda gpSTF N terminal half A map

Fileemd_48256_half_map_1.map
AnnotationBacteriophage Ur-lambda gpSTF N terminal half A map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Bacteriophage Ur-lambda gpSTF N terminal half B map

Fileemd_48256_half_map_2.map
AnnotationBacteriophage Ur-lambda gpSTF N terminal half B map
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 Ur-lambda

EntireName: Escherichia phage Ur-lambda (virus)
Components
  • Virus: Escherichia phage Ur-lambda (virus)
    • Protein or peptide: Tail fiber protein

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Supramolecule #1: Escherichia phage Ur-lambda

SupramoleculeName: Escherichia phage Ur-lambda / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2681611 / Sci species name: Escherichia phage Ur-lambda / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Molecular weightTheoretical: 1 MDa

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Macromolecule #1: Tail fiber protein

MacromoleculeName: Tail fiber protein / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage Lambda (virus)
Molecular weightTheoretical: 10.092285 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAVKISGVLK DGTGKPVQNC TIQLKARRNS TTVVVNTVGS ENPDEAGRYS MDVEYGQYSV ILQVDGFPPS HAGTITVYED SQPGTLNDF LCAMT

UniProtKB: Tail fiber protein

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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: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 1.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 6517
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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