9UKV | pdb_00009ukv

JM Complex - E. coli MurJ, Levivirus M lysis protein LysM (SglM)

• PDB DOI: https://doi.org/10.2210/pdb9UKV/pdb
• EM Map EMD-64256: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Escherichia coli, Enterobacteria phage M
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  MemProtMD


• Deposited: 2025-04-18 Released: 2025-09-10 
• Deposition Author(s): Kohga, H., Lertpreedakorn, N., Tsukazaki, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.05 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Phage lysis protein Lys M acts as a wedge to block MurJ conformational changes.

Kohga, H., Lertpreedakorn, N., Miyazaki, R., Wu, S., Hosoda, K., Tanaka, H., Takahashi, Y.S., Yoshikaie, K., Kuruma, Y., Shigematsu, H., Mori, T., Tsukazaki, T.

(2025) Sci Adv 11: eady8083-eady8083

• PubMed: 41061077 
• DOI: https://doi.org/10.1126/sciadv.ady8083
• Primary Citation Related Structures: 
  9UKV


• PubMed Abstract: 
  

  Many antibiotics target essential cellular processes. To combat multidrug-resistant bacteria, new antibacterial strategies are needed. In the peptidoglycan biogenesis pathway in Escherichia coli , MurJ, the lipid II flippase, is an essential membrane protein. The 37-residue protein M from the Levivirus phage, known as Lys ^M or Sgl ^M , targets MurJ and induces cell lysis; however, its molecular mechanism remains unclear. Here, we present the cryo-EM structure of the MurJ/Lys ^M (JM) complex at 3.09-angstrom resolution, revealing that Lys ^M interacts with the crevasse between TM2 and TM7 of MurJ, locking MurJ in an outward-facing conformation, with Lys ^M acting like a wedge. Alanine-scanning mutagenesis and pull-down assays revealed key residues responsible for Lys ^M function, and molecular dynamics simulations showed that Lys ^M stabilizes MurJ's outward-facing state. These findings demonstrate an unprecedented phage-derived mechanism for blocking lipid II transport, providing a structural framework for designing MurJ-targeted antimicrobial agents.

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Organizational Affiliation: 
• Nara Institute of Science and Technology, Ikoma, Nara, Japan.
Institute for Extra-cutting-edge Science and Technology Avant-garde Research (X-star), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Natsushima-cho, Yokosuka, Kanagawa, Japan.
Structural Biology Division, Japan Synchrotron Radiation Research Institute, SPring-8, Hyogo, Sayo, Japan.
Department of Chemistry, Faculty of Science, Tokyo University of Science, Shinjuku-ku, Tokyo, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 63.64 kDa 
• Atom Count: 4,188 
• Modeled Residue Count: 548 
• Deposited Residue Count: 581 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipid II flippase MurJ	A	534	Escherichia coli	Mutation(s): 0  Gene Names: murJ, mviN, yceN, b1069, JW1056 Membrane Entity: Yes
UniProt
Find proteins for P0AF16 (Escherichia coli (strain K12)) Explore P0AF16  Go to UniProtKB:  P0AF16

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysis protein	B	47	Enterobacteria phage M	Mutation(s): 0  Gene Names: lys
UniProt
Find proteins for K7QK87 (Enterobacteria phage M) Explore K7QK87  Go to UniProtKB:  K7QK87

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.05 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-10 
Deposition Author(s): Kohga, H., Lertpreedakorn, N., Tsukazaki, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2025-09-10
  Type: Initial release
  
• Version 1.1: 2026-03-04
  Changes: Data collection, Database references