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- EMDB-52349: Salmonella enterica Lamassu LmuACB bound to DNA duplex -

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Basic information

Entry
Database: EMDB / ID: EMD-52349
TitleSalmonella enterica Lamassu LmuACB bound to DNA duplex
Map data
Sample
  • Complex: bacterial defence system LmuACB
    • Protein or peptide: ABC-three component systems C-terminal domain-containing protein
    • Protein or peptide: DUF3732 domain-containing protein
    • DNA: DNA (29-MER)
    • DNA: DNA (29-MER)
    • Protein or peptide: LmuC
KeywordsLamassu / Rad50 / Cap4 / bacterial immunity / defence system / DNA end binding / ABC ATPase / SMC-like / Cap4 nuclease / phage / plasmid restriction / IMMUNE SYSTEM
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) / Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsLi Y / Gruber S
Funding support Switzerland, 1 items
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, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52349.png

Downloads & links

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Map

FileDownload / File: emd_52349.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 400 pix.
= 290.4 Å		0.73 Å/pix.
x 400 pix.
= 290.4 Å		0.73 Å/pix.
x 400 pix.
= 290.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.726 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0384
Minimum - Maximum-0.38096762 - 0.6369348
Average (Standard dev.)0.00016024773 (±0.011210167)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 290.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52349_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Half map: #2

Fileemd_52349_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_52349_half_map_2.map
Projections & Slices
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Sample components

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Entire : bacterial defence system LmuACB

EntireName: bacterial defence system LmuACB
Components
  • Complex: bacterial defence system LmuACB
    • Protein or peptide: ABC-three component systems C-terminal domain-containing protein
    • Protein or peptide: DUF3732 domain-containing protein
    • DNA: DNA (29-MER)
    • DNA: DNA (29-MER)
    • Protein or peptide: LmuC

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Supramolecule #1: bacterial defence system LmuACB

SupramoleculeName: bacterial defence system LmuACB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1, #4-#5, #3
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Tennessee (bacteria)

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Macromolecule #1: DUF3732 domain-containing protein

MacromoleculeName: DUF3732 domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Tennessee (bacteria)
Strain: TXSC_TXSC08-19
Molecular weightTheoretical: 75.235875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYFQIRGIIL WPRNKNFKPH TIRFELGKVN VISGASRTGK SAVIPIIDYC LGANTCSIPV KTIRKYCEWF GIVVATEQGE KLLARKEPG NQRSTTDMFV LEAENITSIP IRLEKNTNVI AVKRMLDDLA NLSNLDFSGG DENSGFDGRP AFRDLAAFTF Q PQNVVANP ...String:
MYFQIRGIIL WPRNKNFKPH TIRFELGKVN VISGASRTGK SAVIPIIDYC LGANTCSIPV KTIRKYCEWF GIVVATEQGE KLLARKEPG NQRSTTDMFV LEAENITSIP IRLEKNTNVI AVKRMLDDLA NLSNLDFSGG DENSGFDGRP AFRDLAAFTF Q PQNVVANP DVLFFKTNTY EHREKLRKIF PYVLGAITSE LMAKQFELNR IRLFLRRKER ELKDAQDVSA QWLADLKSKY SE AQELGLV PKPQEQLSRK QMISQLEEVI SRTDLTLKVT VSTISDALSE LNTLESEERL VSRELTTMRH RLEEMNRLRV GMH QYENAL LMQRDRLKIS GWLLSNTNDE SDCPMCGSHT DSAKQKLQAL VQRLSDVEAA VGADAHKEVP AAFDRELQRV TTEV ANATE RLRAIQSRKR TLTSRSKEAR EQQFSTRRAE RFIGNVESAL ELHRKLGSDS ELVEEVRKLK EMVQTLEKEL REKDV ELRK NQALRVINAQ AGNILQGLDV EDPSAPISLE INDLTIKVLG DERDDYLSEI GSGSNWLSYH LAILLSLHQF YLSQKN NPV PSFLILDQPS QVYFPKTTQL PNIANEDEPK LRDEDVEAVR RAFKAMGNVV IKEKGKLQLI VLDHAPREVW GEIDGVV GL PEWRDGIKLV PMEWLTGV

UniProtKB: DUF3732 domain-containing protein

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Macromolecule #2: ABC-three component systems C-terminal domain-containing protein

MacromoleculeName: ABC-three component systems C-terminal domain-containing protein
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Tennessee (bacteria)
Strain: TXSC_TXSC08-19
Molecular weightTheoretical: 45.323305 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAISKTNGQS KPKRKTEVPG QALGYSLQFT LLTHLLLQAP EGSLCSLEVL DDVAQENNSG DIKFIQSASA LTANPAADRA KSLWKTLSN WIDLATSPDF EVEKAIFELY VSRPVEGSIV KKFNEAKTPE DAQEAITHAR TELWGDSPHF TLKDGISKEI S KYVEKVFT ...String:
MAISKTNGQS KPKRKTEVPG QALGYSLQFT LLTHLLLQAP EGSLCSLEVL DDVAQENNSG DIKFIQSASA LTANPAADRA KSLWKTLSN WIDLATSPDF EVEKAIFELY VSRPVEGSIV KKFNEAKTPE DAQEAITHAR TELWGDSPHF TLKDGISKEI S KYVEKVFT ADQNLLQRLI CNFQLTLGSG SPQADLEACV RSHPVSPSKV SDITNYLCGK VKRHIDMLLE AEKPAVIARD DF YTWYKAY VQKIDRQMVL SSRAQAPVKE KAQEYLPDKF VQQLEIIGLP YEEILGAISD YLMASFDRTD WAARGEVDET SFD DLDTAL QRTWKNKQRI CGLTHSEKSE QDQGKLLYFE CMQFNIPLQA MSPPSHFIPG CYHILADSLA VGWHPNYTTQ LKNK KVA

UniProtKB: ABC-three component systems C-terminal domain-containing protein

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Macromolecule #3: LmuC

MacromoleculeName: LmuC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Tennessee (bacteria)
Molecular weightTheoretical: 18.377428 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLAREAQNIQ NPALGAALVW RFCCGYVKTN RVSAPPPLPF LFLVLPIILH QETSEFVKRT YKSSGLRAFA AKFGDSSVSK QDLLFQIHE RSIRWRQLSL RSIELAVASD LLKLQDGSDV IPLSKTKARG LSDEVKTLMD LAEKLGSWFG ELSIHEVVTT L KVKL

UniProtKB: Uncharacterized protein

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Macromolecule #4: DNA (29-MER)

MacromoleculeName: DNA (29-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 8.855751 KDa
SequenceString:
(DA)(DT)(DC)(DT)(DC)(DG)(DA)(DT)(DA)(DA) (DC)(DT)(DC)(DA)(DA)(DA)(DA)(DA)(DA)(DT) (DA)(DC)(DG)(DC)(DC)(DC)(DG)(DG)(DT)

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Macromolecule #5: DNA (29-MER)

MacromoleculeName: DNA (29-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Bacillus subtilis subsp. subtilis str. 168 (bacteria)
Molecular weightTheoretical: 8.970776 KDa
SequenceString:
(DA)(DC)(DC)(DG)(DG)(DG)(DC)(DG)(DT)(DA) (DT)(DT)(DT)(DT)(DT)(DT)(DG)(DA)(DG)(DT) (DT)(DA)(DT)(DC)(DG)(DA)(DG)(DA)(DT)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135346
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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