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- EMDB-49934: LmuABC-DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-49934
TitleLmuABC-DNA
Map data
Sample
  • Complex: LmuABC-DNA
    • Protein or peptide: LmuC
    • Protein or peptide: ABC-three component systems C-terminal domain-containing protein
    • Protein or peptide: DUF3732 domain-containing protein
    • DNA: DNA
    • DNA: DNA
KeywordsLmuABC-DNA / DNA BINDING PROTEIN-DNA complex
Function / homologyProtein 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 / DUF3732 domain-containing protein / ABC-three component systems C-terminal domain-containing protein / Uncharacterized protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsChakravarti A / Zhang Z
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural basis for Lamassu-based antiviral immunity and its evolution from DNA repair machinery.
Authors: Matthieu Haudiquet / Arpita Chakravarti / Zhiying Zhang / Josephine L Ramirez / Alba Herrero Del Valle / Paul Dominic B Olinares / Rachel Lavenir / Massilia Aït Ahmed / M Jason de la Cruz / ...Authors: Matthieu Haudiquet / Arpita Chakravarti / Zhiying Zhang / Josephine L Ramirez / Alba Herrero Del Valle / Paul Dominic B Olinares / Rachel Lavenir / Massilia Aït Ahmed / M Jason de la Cruz / Brian T Chait / Samuel H Sternberg / Aude Bernheim / Dinshaw J Patel /
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 ...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 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.
History
DepositionMar 27, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49934.png

Downloads & links

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Map

FileDownload / File: emd_49934.map.gz / Format: CCP4 / Size: 421.9 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 480 pix.
= 348. Å		0.73 Å/pix.
x 480 pix.
= 348. Å		0.73 Å/pix.
x 480 pix.
= 348. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0739
Minimum - Maximum-0.48176783 - 0.76388246
Average (Standard dev.)-0.0000070192996 (±0.010605755)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 348.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49934_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49934_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : LmuABC-DNA

EntireName: LmuABC-DNA
Components
  • Complex: LmuABC-DNA
    • Protein or peptide: LmuC
    • Protein or peptide: ABC-three component systems C-terminal domain-containing protein
    • Protein or peptide: DUF3732 domain-containing protein
    • DNA: DNA
    • DNA: DNA

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Supramolecule #1: LmuABC-DNA

SupramoleculeName: LmuABC-DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)

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Macromolecule #1: LmuC

MacromoleculeName: LmuC / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 20.310744 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIKNLEIQML KPENNLEKEA WEINNPAMCS YMLWIATLAY YQKQKEPIHP SRLFCLFPFI LYSDTRNVLL SSKGSLKSYL AKFSNSKAI SGDIPLSIHF RIDIQKNKTL DALIVAFDSG LLVIDSDSGL IKPNVSIKPL PNSKLTDTIK ELVYCSTKIG R WLSEMTNQ DLARDLKVIF

UniProtKB: Uncharacterized 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: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 44.584719 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKDNSTSAVS SWLGYKIQEY RLTQRLLEAN NSSCIGFEIL DDLEEHTGST STFEQDKIST TGRNIVSNHS KDLWKTLSNW MDLIDSGEI DVDNTIFLLF TNKRCHSEVL QLLSTSQATE EASKAFDEIL KIVSHPSPSI ANYLNNFSKS KTDACRLISK F TYIYGSGS ...String:
MKDNSTSAVS SWLGYKIQEY RLTQRLLEAN NSSCIGFEIL DDLEEHTGST STFEQDKIST TGRNIVSNHS KDLWKTLSNW MDLIDSGEI DVDNTIFLLF TNKRCHSEVL QLLSTSQATE EASKAFDEIL KIVSHPSPSI ANYLNNFSKS KTDACRLISK F TYIYGSGS APHDLRESYK LHRLGALEEH LDEIMYEILG WVSDVLTLAA EKRQPTIVRA KDFGARLGEI ESKYRQKTIL NY FCNRSSE SEDVQNTIKD APNYIKQLNL INVDDSELEE AAIANLETKD AVVEWTLNGD VQDYSYRYYQ RELRRCWGIQ KQK IHLDFN GRPETEVGQR LYIECLNNVT RYYLENKKVG DFFAHGTLHS MADKLTIGWH PEFDKKLGDP DA

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

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Macromolecule #3: DUF3732 domain-containing protein

MacromoleculeName: DUF3732 domain-containing protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 74.726055 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFFQIEKVVL WSKEAKHKPR VIEFALNKVN LITGSSKSGK SSLIPIIDYC LGSSKCSIPV NTIRDTTAWY GVQIKTKHSR LLIARRDPS NQLSTSNAFF VEAENIEIPQ NIEKHNVNID TVKNRLNEIS GVSNISFDFY DTGRIDKKRT STRDLSAFNY Q PQNIIANP ...String:
MFFQIEKVVL WSKEAKHKPR VIEFALNKVN LITGSSKSGK SSLIPIIDYC LGSSKCSIPV NTIRDTTAWY GVQIKTKHSR LLIARRDPS NQLSTSNAFF VEAENIEIPQ NIEKHNVNID TVKNRLNEIS GVSNISFDFY DTGRIDKKRT STRDLSAFNY Q PQNIIANP NALFYKTDSF EHKSKLVTIL PYVLGALSNT DIENQHRIKN LEEEYRKVER RLLKLKRQNE DWLSSAQAYV IK AMELGLV NSDKDIYQLK PERLLNVLKN IATKEIDYST SAANIKYASE QEAEITKRSR DISNNLAKVK SRLQNINSMN RLA NTHSDA SRLKRERLSL SKWLLTQNDI NSSLFSEPNE IRSLVLEPLA RAFSNLEAEL EVPIHVQGAL SREKIYLEGE LTRL ASEMK DVNTQLKILR GNKRKLGYDA FSVGKFVGEV EKALSLMGES ESESELSKEY KRLKKELSVL RLKIDPREFE RKTKL QLAK VNKLASDWLP HLDTENPNAP ISLHEKELTI TVNSSGREDY LWEIGSGANW LSYHVAITLA LHQHFSSLEA SPVPNY IIY DQPSQVYFPS KLRHQATPEE DELALLEQDE DIVQVKKIFE AFNGAIEKTK DNLQIIVLDH APSTLVKSIP KGHLVEE WR NGIKLIPLDW L

UniProtKB: DUF3732 domain-containing protein

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Macromolecule #4: DNA

MacromoleculeName: DNA / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 6.221065 KDa
SequenceString:
(DG)(DT)(DG)(DA)(DT)(DA)(DG)(DT)(DT)(DA) (DG)(DA)(DA)(DA)(DC)(DG)(DT)(DA)(DA)(DT)

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Macromolecule #5: DNA

MacromoleculeName: DNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 5.121348 KDa
SequenceString:
(DA)(DC)(DG)(DT)(DT)(DT)(DC)(DT)(DA)(DA) (DC)(DT)(DA)(DT)(DC)(DA)(DC)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 190887
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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