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- PDB-9ux7: CryoEM Structure of LmuAB-DNA complex -

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Basic information

Entry
Database: PDB / ID: 9ux7
TitleCryoEM Structure of LmuAB-DNA complex
Components
  • (DNA (41-MER)) x 2
  • Lamassu protein LmuA
  • Lamassu protein LmuB
KeywordsIMMUNE SYSTEM / complex / anti-phage system
Function / homology
Function and homology information


nuclease activity / defense response to virus / hydrolase activity
Similarity search - Function
CD-NTase associated protein 4, DNA endonuclease domain / Cap4, dsDNA endonuclease domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / Lamassu protein LmuA / Lamassu protein LmuB
Similarity search - Component
Biological speciesBacillus sp. nio-1130 (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.73 Å
AuthorsLi, M. / Zhao, X. / An, L. / Li, S. / Zhang, K. / Feng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: Nat Chem Biol / Year: 2026
Title: Structural insights into type-I and type-II Lamassu antiphage systems.
Authors: Ming Li / Xiaolong Zhao / Xingyu Zhao / Dong Li / Weijia Xiong / Zirui Gao / Ling Huang / Linfeng An / Yongxiang Gao / Shanshan Li / Yue Feng / Kaiming Zhang / Yi Zhang /
Abstract: Bacteria have developed a variety of immune systems to combat phage infections. The Lamassu system is a prokaryotic immune system with a core conserved structural maintenance of chromosomes (SMC) ...Bacteria have developed a variety of immune systems to combat phage infections. The Lamassu system is a prokaryotic immune system with a core conserved structural maintenance of chromosomes (SMC) superfamily protein LmuB and diverse effectors named LmuA, whose mechanism remains unclear. Here we present a series of cryo-electron microscopy structures of the type-I Lamassu complex from Bacillus cellulasensis and the type-II Lamassu complex from Vibrio cholerae, both in apo and dsDNA-bound states, revealing an unexpected stoichiometry and topological architecture distinct from canonical SMC complexes. Combined structural and biochemical analyses show how the nuclease effector LmuA is sequestered in an inactive monomeric form within the Lamassu complex and, upon sensing foreign DNA ends, dissociates and assembles into an active tetramer capable of DNA cleavage. Our findings elucidate the mechanism by which Lamassu systems detect viral replication and implement antiphage defense, highlighting the roles of SMC proteins in prokaryotic immunity.
History
DepositionMay 13, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lamassu protein LmuB
B: Lamassu protein LmuB
C: Lamassu protein LmuA
D: DNA (41-MER)
E: DNA (41-MER)


Theoretical massNumber of molelcules
Total (without water)194,3615
Polymers194,3615
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Lamassu protein LmuB / Putative ATPase LmuB


Mass: 66507.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. nio-1130 (bacteria) / Gene: lmuB, AS035_15075 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DW44
#2: Protein Lamassu protein LmuA


Mass: 36103.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. nio-1130 (bacteria) / Gene: lmuA, AS035_15080 / Production host: Escherichia coli (E. coli) / References: UniProt: P0DW43
#3: DNA chain DNA (41-MER)


Mass: 12594.122 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#4: DNA chain DNA (41-MER)


Mass: 12647.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CryoEM structure of LmuAB-DNA complex / Type: COMPLEX / Entity ID: #1-#2, #4 / Source: RECOMBINANT
Molecular weightValue: 0.18 MDa / Experimental value: YES
Source (natural)Organism: Bacillus sp. (strain NCIM 5461 / CCTCC AB 2011126 / NIO-1130) (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3100 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 50.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
8PHENIXmodel refinement
12cryoSPARC3.2classification
13cryoSPARC4.23D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1144023
3D reconstructionResolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 437756 / Symmetry type: POINT
RefinementHighest resolution: 3.73 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313883
ELECTRON MICROSCOPYf_angle_d0.62519032
ELECTRON MICROSCOPYf_dihedral_angle_d18.7832346
ELECTRON MICROSCOPYf_chiral_restr0.0412151
ELECTRON MICROSCOPYf_plane_restr0.0042125

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