9MGH | pdb_00009mgh

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

• PDB DOI: https://doi.org/10.2210/pdb9MGH/pdb
• EM Map EMD-48256: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Escherichia phage Lambda
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2024-12-10 Released: 2025-11-26 
• Deposition Author(s): Yu, H., Liu, J., Molineux, I.J.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.31 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 41237242 
• 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.

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Organizational Affiliation: 
• Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.
Microbial Sciences Institute, Yale University, West Haven, CT, USA.
LaMontagne Center for Infectious Disease, Institute for Cell and Molecular Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C12  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 121.11 kDa 
• Atom Count: 8,448 
• Modeled Residue Count: 1,128 
• Deposited Residue Count: 1,128 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tail fiber protein	A [auth Ta], B [auth Tb], C [auth Tc], D [auth Td], E [auth Te], F [auth Tf], G [auth Tg], H [auth Th], I [auth Ti], J [auth Tj], K [auth Tk], L [auth Tl]	94	Escherichia phage Lambda	Mutation(s): 0  Gene Names: stf, lambdap27
UniProt
Find proteins for P03764 (Escherichia phage lambda) Explore P03764  Go to UniProtKB:  P03764

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.31 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5190
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Yu, H., Liu, J., Molineux, I.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	124378
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	110243

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release