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- PDB-9mgh: In situ cryo-EM structure of bacteriophage Ur-lambda tail side fiber -

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Basic information

Entry
Database: PDB / ID: 9mgh
TitleIn situ cryo-EM structure of bacteriophage Ur-lambda tail side fiber
ComponentsTail fiber protein
KeywordsVIRAL PROTEIN / bacteriophage / tail tip complex
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsYu, H. / Liu, J. / Molineux, I.J.
Funding support United States, 2items
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, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Ta: Tail fiber protein
Tb: Tail fiber protein
Tc: Tail fiber protein
Td: Tail fiber protein
Te: Tail fiber protein
Tf: Tail fiber protein
Tg: Tail fiber protein
Th: Tail fiber protein
Ti: Tail fiber protein
Tj: Tail fiber protein
Tk: Tail fiber protein
Tl: Tail fiber protein


Theoretical massNumber of molelcules
Total (without water)121,10712
Polymers121,10712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Tail fiber protein / stf / Gene product 27 / gp27


Mass: 10092.285 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage Lambda (virus) / Gene: stf, lambdap27 / Production host: Escherichia coli (E. coli) / References: UniProt: P03764
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Escherichia phage Ur-lambda / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)Organism: Escherichia phage Ur-lambda (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1600 nm / Calibrated defocus max: 1000 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21_5190model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6517 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 86.08 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00398580
ELECTRON MICROSCOPYf_angle_d0.630711664
ELECTRON MICROSCOPYf_chiral_restr0.04891368
ELECTRON MICROSCOPYf_plane_restr0.00451536
ELECTRON MICROSCOPYf_dihedral_angle_d4.3721200

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