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- EMDB-64583: type II Lamassu, LmuACB with DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-64583
Titletype II Lamassu, LmuACB with DNA
Map data
Sample
  • Complex: Cryo-EM structure of VcLmuACB-DNA complex
    • DNA: DNA (59-MER)
    • DNA: DNA (59-MER)
    • Protein or peptide: DUF3732 domain-containing protein
    • Protein or peptide: ABC-three component systems C-terminal domain-containing protein
    • Protein or peptide: Lamassu C
Keywordsendonuclease / Structural maintenance of chromosomes (SMC) proteins / DNA BINDING PROTEIN
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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsZhao X / Li M / Li S / Feng Y / Zhang K
Funding support1 items
OrganizationGrant numberCountry
Other government
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 14, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64583.png

Downloads & links

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Map

FileDownload / File: emd_64583.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.08256244 - 0.19827177
Average (Standard dev.)0.000016862894 (±0.0043767737)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_64583_additional_1.map
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Half map: #2

Fileemd_64583_half_map_1.map
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Half map: #1

Fileemd_64583_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of VcLmuACB-DNA complex

EntireName: Cryo-EM structure of VcLmuACB-DNA complex
Components
  • Complex: Cryo-EM structure of VcLmuACB-DNA complex
    • DNA: DNA (59-MER)
    • DNA: DNA (59-MER)
    • Protein or peptide: DUF3732 domain-containing protein
    • Protein or peptide: ABC-three component systems C-terminal domain-containing protein
    • Protein or peptide: Lamassu C

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Supramolecule #1: Cryo-EM structure of VcLmuACB-DNA complex

SupramoleculeName: Cryo-EM structure of VcLmuACB-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 202.7 KDa

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Macromolecule #1: DNA (59-MER)

MacromoleculeName: DNA (59-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 18.214699 KDa
SequenceString: (DC)(DG)(DC)(DT)(DT)(DT)(DA)(DT)(DC)(DA) (DG)(DA)(DA)(DG)(DC)(DC)(DA)(DG)(DA)(DC) (DA)(DT)(DT)(DA)(DA)(DC)(DG)(DC)(DT) (DT)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DA) (DC) (DT)(DC)(DA)(DA)(DC)(DG) ...String:
(DC)(DG)(DC)(DT)(DT)(DT)(DA)(DT)(DC)(DA) (DG)(DA)(DA)(DG)(DC)(DC)(DA)(DG)(DA)(DC) (DA)(DT)(DT)(DA)(DA)(DC)(DG)(DC)(DT) (DT)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DA) (DC) (DT)(DC)(DA)(DA)(DC)(DG)(DA)(DG) (DC)(DT)(DG)(DG)(DA)(DC)(DG)(DC)(DG)(DG) (DA)

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Macromolecule #2: DNA (59-MER)

MacromoleculeName: DNA (59-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 18.151602 KDa
SequenceString: (DT)(DC)(DC)(DG)(DC)(DG)(DT)(DC)(DC)(DA) (DG)(DC)(DT)(DC)(DG)(DT)(DT)(DG)(DA)(DG) (DT)(DT)(DT)(DC)(DT)(DC)(DC)(DA)(DG) (DA)(DA)(DG)(DC)(DG)(DT)(DT)(DA)(DA)(DT) (DG) (DT)(DC)(DT)(DG)(DG)(DC) ...String:
(DT)(DC)(DC)(DG)(DC)(DG)(DT)(DC)(DC)(DA) (DG)(DC)(DT)(DC)(DG)(DT)(DT)(DG)(DA)(DG) (DT)(DT)(DT)(DC)(DT)(DC)(DC)(DA)(DG) (DA)(DA)(DG)(DC)(DG)(DT)(DT)(DA)(DA)(DT) (DG) (DT)(DC)(DT)(DG)(DG)(DC)(DT)(DT) (DC)(DT)(DG)(DA)(DT)(DA)(DA)(DA)(DG)(DC) (DG)

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

MacromoleculeName: ABC-three component systems C-terminal domain-containing protein
type: protein_or_peptide / ID: 4 / 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 #5: Lamassu C

MacromoleculeName: Lamassu C / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 19.339545 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLKPENNLEK EAWEINNPAM CSYMLWIATL AYYQKQKEPI HPSRLFCLFP FILYSDTRNV LLSSKGSLKS YLAKFSNSKA ISGDIPLSI HFRIDIQKNK TLDALIVAFD SGLLVIDSDS GLIKPNVSIK PLPNSKLTDT IKELVYCSTK IGRWLSEMTN Q DLARDLKV IF

UniProtKB: Uncharacterized protein

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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: GATAN K3 (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.1 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 122544
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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