9NYG | pdb_00009nyg

LmuABC-DNA


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis for Lamassu-based antiviral immunity and its evolution from DNA repair machinery.

Haudiquet, M.Chakravarti, A.Zhang, Z.Ramirez, J.L.Herrero Del Valle, A.Olinares, P.D.B.Lavenir, R.Ahmed, M.A.de la Cruz, M.J.Chait, B.T.Sternberg, S.H.Bernheim, A.Patel, D.J.

(2025) Proc Natl Acad Sci U S A 122: e2519643122-e2519643122

  • DOI: https://doi.org/10.1073/pnas.2519643122
  • Primary Citation of Related Structures:  
    9NXX, 9NY1, 9NY5, 9NYG

  • PubMed Abstract: 

    Bacterial immune systems exhibit remarkable diversity and modularity, as a consequence of the continuous selective pressures imposed by phage predation. Despite recent mechanistic advances, the evolutionary origins of many antiphage immune systems remain elusive, especially for those that encode homologs of the structural maintenance of chromosomes (SMC) superfamily, which are essential for chromosome maintenance and DNA repair across domains of life. Here, we elucidate the structural basis and evolutionary emergence of Lamassu, a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor. Using cryo-EM, we determined structures of the Vibrio cholerae Lamassu complex in both apo- and dsDNA-bound states, revealing unexpected stoichiometry and topological architectures. We further demonstrate how Lamassu specifically senses dsDNA ends in vitro and phage replication origins in vivo, thereby triggering the formation of LmuA tetramers that activate its Cap4 nuclease domain. Our findings reveal that Lamassu evolved via exaptation of the bacterial Rad50-Mre11 DNA repair system to form a compact, modular sensor for viral replication, exemplifying how cellular machinery can be co-opted for novel immune functions.


  • Organizational Affiliation
    • Institut Pasteur, Université Paris-Cité, CNRS UMR2535, Department of Genomes and Genetics, Molecular Diversity of Microbes, Paris 75015, France.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LmuCA [auth C]178Vibrio choleraeMutation(s): 0 
Gene Names: D6U24_12490VC_0491
UniProt
Find proteins for A0A060KYQ4 (Vibrio cholerae)
Explore A0A060KYQ4 
Go to UniProtKB:  A0A060KYQ4
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UniProt GroupA0A060KYQ4
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ABC-three component systems C-terminal domain-containing proteinB [auth A]388Vibrio choleraeMutation(s): 0 
Gene Names: D6U24_12485ERS013200_03523ERS013201_03639KIN13_15850VC_0492
UniProt
Find proteins for A0A060KT36 (Vibrio cholerae)
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Go to UniProtKB:  A0A060KT36
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UniProt GroupA0A060KT36
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DUF3732 domain-containing proteinC [auth G],
D [auth B]
653Vibrio choleraeMutation(s): 0 
Gene Names: D6U24_12495ERS013200_03521ERS013201_03641KIN13_15860VC_0490
UniProt
Find proteins for A0A060KSR0 (Vibrio cholerae)
Explore A0A060KSR0 
Go to UniProtKB:  A0A060KSR0
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UniProt GroupA0A060KSR0
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  • Reference Sequence

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Entity ID: 4
MoleculeChains LengthOrganismImage
DNA20Vibrio cholerae
Sequence Annotations
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  • Reference Sequence

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Entity ID: 5
MoleculeChains LengthOrganismImage
DNA17Vibrio cholerae
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-17
    Type: Initial release