9E7M | pdb_00009e7m

In situ cryoEM structure of bacteriophage Ur-lambda tail tip complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of bacteriophage Ur-lambda infection initiation.

Yu, H.Wang, C.Yue, J.Guo, W.Molineux, I.J.Liu, J.

(2025) Sci Adv 11: eadw7914-eadw7914

  • DOI: https://doi.org/10.1126/sciadv.adw7914
  • Primary Citation of Related Structures:  
    9E7M, 9MGH

  • PubMed 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-electron microscopy and tomography to visualize infection initiation by Ur-λ, the original λ isolate that uses side fibers to adsorb rapidly to Escherichia coli . 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.


  • Organizational Affiliation
    • Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tape measure proteinA [auth Ha],
C [auth Hb],
E [auth Hc]
32Escherichia phage LambdaMutation(s): 0 
Gene Names: Hlambdap16
UniProt
Find proteins for P03736 (Escherichia phage lambda)
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Go to UniProtKB:  P03736
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UniProt GroupP03736
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tail tip assembly protein IB [auth Ia],
D [auth Ib]
90Escherichia phage LambdaMutation(s): 0 
Gene Names: Ilambdap20
UniProt
Find proteins for P03730 (Escherichia phage lambda)
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Go to UniProtKB:  P03730
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UniProt GroupP03730
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tail tip assembly protein IF [auth Ic]90Escherichia phage LambdaMutation(s): 0 
Gene Names: Ilambdap20
UniProt
Find proteins for P03730 (Escherichia phage lambda)
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UniProt GroupP03730
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tip attachment protein JG [auth Ja],
H [auth Jb],
I [auth Jc]
835Escherichia phage LambdaMutation(s): 0 
Gene Names: Jlambdap21
UniProt
Find proteins for P03749 (Escherichia phage lambda)
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UniProt GroupP03749
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Tail tip protein LJ [auth Lc],
K [auth Lb],
L [auth La]
232Escherichia phage LambdaMutation(s): 0 
Gene Names: Llambdap18
UniProt
Find proteins for P03738 (Escherichia phage lambda)
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UniProt GroupP03738
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Tail fiber protein94Escherichia phage LambdaMutation(s): 0 
Gene Names: stflambdap27
UniProt
Find proteins for P03764 (Escherichia phage lambda)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Tail tip protein M109Escherichia phage LambdaMutation(s): 0 
Gene Names: Mlambdap17
UniProt
Find proteins for P03737 (Escherichia phage lambda)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Tail tube protein152Escherichia phage LambdaMutation(s): 0 
Gene Names: Vlambdap13
UniProt
Find proteins for P03733 (Escherichia phage lambda)
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5190

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States124378
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States110243

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-05
    Type: Initial release
  • Version 1.1: 2025-11-26
    Changes: Data collection, Database references