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- PDB-9hqu: Salmonella enterica Lamassu LmuACB in nuclease sequestration state -

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Basic information

Entry
Database: PDB / ID: 9hqu
TitleSalmonella enterica Lamassu LmuACB in nuclease sequestration state
Components
  • ABC-three component systems C-terminal domain-containing protein
  • DUF3732 domain-containing protein
  • LmuC
KeywordsIMMUNE SYSTEM / Lamassu / Rad50 / Cap4 / bacterial immunity / defence system / DNA end binding / ABC ATPase / SMC-like / Cap4 nuclease / phage / plasmid restriction
Function / homology
Function and homology information


Protein of unknown function DUF3732 / ABC-three component system, Middle Component 3 / Protein of unknown function (DUF3732) / ABC-three component (ABC-3C) system Middle Component 3 / ABC-three component systems, C-terminal domain 7 / C-terminal domain 7 of the ABC-three component (ABC-3C) systems / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DUF3732 domain-containing protein / ABC-three component systems C-terminal domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Tennessee (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsLi, Y. / Gruber, S.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation320030-227915 Switzerland
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structure and activation mechanism of a Lamassu phage and plasmid defense system.
Authors: Yan Li / David W Adams / Hon Wing Liu / Steven J Shaw / Emiko Uchikawa / Milena Jaskólska / Sandrine Stutzmann / Laurie Righi / Mark D Szczelkun / Melanie Blokesch / Stephan Gruber /
Abstract: Lamassu is a diverse family of defense systems that protect bacteria, including seventh-pandemic strains of Vibrio cholerae, against both plasmids and phage infection. During phage infection, Lamassu ...Lamassu is a diverse family of defense systems that protect bacteria, including seventh-pandemic strains of Vibrio cholerae, against both plasmids and phage infection. During phage infection, Lamassu targets essential cellular processes, thereby halting phage propagation by terminating the infected host. The mechanisms by which Lamassu effectors are activated when needed and otherwise suppressed are unknown. Here we present structures of a Lamassu defense system from Salmonella enterica. We show that an oligomerization domain of the nuclease effector subunit, LmuA, is sequestered by two tightly folded SMC-like LmuB protomers and LmuC. Upon activation, liberated LmuA assembles into homotetramers, in which two of four nuclease domains are brought into proximity to create an active site capable of cleaving DNA. We propose that tetramer formation is likely a one-way switch that establishes a threshold to limit potential spontaneous activation and cell death. Our findings reveal a mechanism of cellular defense, involving liberation and oligomerization of immune effectors, and shed light on how Lamassu systems balance potent immune responses with self-preservation.
History
DepositionDec 17, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUF3732 domain-containing protein
B: DUF3732 domain-containing protein
C: ABC-three component systems C-terminal domain-containing protein
D: LmuC


Theoretical massNumber of molelcules
Total (without water)214,2314
Polymers214,2314
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein DUF3732 domain-containing protein


Mass: 75235.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Tennessee (bacteria)
Strain: TXSC_TXSC08-19
Gene: AHW86_02670, B1277_19175, CC786_01560, DKV27_15540, E0563_21155, FG623_013450, GB216_17200
Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G3DSI6
#2: Protein ABC-three component systems C-terminal domain-containing protein


Mass: 45381.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Tennessee (bacteria)
Strain: TXSC_TXSC08-19
Gene: AHW86_02680, B1277_19165, CC786_01570, DKV27_15550, E0563_21145, FG623_013460, GB216_17210
Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G3DTP5
#3: Protein LmuC


Mass: 18377.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Tennessee (bacteria)
Strain: TXSC_TXSC08-19
Gene: AHW86_02675, B1277_19170, CC786_01565, DKV27_15545, E0563_21150, FG623_013455, GB216_17205
Production host: Escherichia coli (E. coli) / References: UniProt: A0A3G3DTV8
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: LmuACB / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Tennessee (bacteria)
Strain: TXSC_TXSC08-19
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Details: 150 mM NaCl, 20mM HEPES, pH7.5, 1mM Tcep, 5mM MgCl2, 1mM ATP, 0.05% b-OG
Buffer componentConc.: 150 mM / Name: Sodium Chloride / Formula: NaCl
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
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: 1500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 242023 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 140.44 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003912919
ELECTRON MICROSCOPYf_angle_d0.519917444
ELECTRON MICROSCOPYf_chiral_restr0.03751977
ELECTRON MICROSCOPYf_plane_restr0.00432258
ELECTRON MICROSCOPYf_dihedral_angle_d4.43061732

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