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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: Li, M. / Zhao, X. / Zhao, X. / Li, D. / Xiong, W. / Gao, Z. / Huang, L. / An, L. / Gao, Y. / Li, S. / Feng, Y. / Zhang, K. / Zhang, Y.
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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