9J1J | pdb_00009j1j

Cap region of monocin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of an F-type phage tail-like bacteriocin from Listeria monocytogenes.

Gu, Z.Ge, X.Wang, J.

(2025) Nat Commun 16: 1695-1695

  • DOI: https://doi.org/10.1038/s41467-025-57075-3
  • Primary Citation of Related Structures:  
    9J1J, 9J1K, 9J1L

  • PubMed Abstract: 

    F-type phage tail-like bacteriocins (PTLBs) are high-molecular-weight protein complexes exhibiting bactericidal activity and share evolutionary similarities with the tails of non-contractile siphoviruses. In this study, we present the atomic structure of monocin, a genetically engineered F-type PTLB from Listeria monocytogenes. Our detailed atomic-level analysis, excluding two chaperone proteins, provides crucial insights into the molecular architecture of F-type PTLBs. The core structure of monocin resembles TP901-1-like phage tails, featuring three side fibers with receptor-binding domains that connect to the baseplate for host adhesion. Based on these findings, we propose a potential mechanism by which F-type PTLBs induce cell death, offering a foundation for developing targeted antibacterial therapies.


  • Organizational Affiliation

    State Key Laboratory of Membrane Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, PR China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AA protein170Listeria monocytogenesMutation(s): 0 
Gene Names: 
UniProt
Find proteins for O05551 (Listeria monocytogenes)
Explore O05551 
Go to UniProtKB:  O05551
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO05551
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DUF5072 domain-containing protein129Listeria monocytogenesMutation(s): 0 
Gene Names: AP104_04165B4X68_12545
UniProt
Find proteins for A0A9P1T1V5 (Listeria monocytogenes)
Explore A0A9P1T1V5 
Go to UniProtKB:  A0A9P1T1V5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A9P1T1V5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32371254
National Natural Science Foundation of China (NSFC)China32171190

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-08
    Type: Initial release
  • Version 1.1: 2025-02-26
    Changes: Data collection, Database references
  • Version 1.2: 2025-03-05
    Changes: Data collection, Database references
  • Version 1.3: 2025-07-16
    Changes: Data collection