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- EMDB-64585: type II Lamassu, LmuACB from Vibrio cholerae O1 El -

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Basic information

Entry
Database: EMDB / ID: EMD-64585
Titletype II Lamassu, LmuACB from Vibrio cholerae O1 El
Map dataCryo-EM map of DdmABC with partial structure
Sample
  • Complex: Cryo-EM structure of VcLmuACB complex
    • 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.54 Å
AuthorsZhao X / Li M / Li S / Feng Y / Zhang K / Liu L
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
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_64585.png

Downloads & links

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Map

FileDownload / File: emd_64585.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of DdmABC with partial structure
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å		0.82 Å/pix.
x 336 pix.
= 275.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.12910233 - 0.32826278
Average (Standard dev.)-0.000107303196 (±0.008379206)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 275.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryo-EM sharp map of DdmABC with partial structure

Fileemd_64585_additional_1.map
AnnotationCryo-EM sharp map of DdmABC with partial structure
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half A map of DdmABC with partial structure

Fileemd_64585_half_map_1.map
AnnotationCryo-EM half A map of DdmABC with partial structure
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half B map of DdmABC with partial structure

Fileemd_64585_half_map_2.map
AnnotationCryo-EM half B map of DdmABC with partial structure
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of VcLmuACB complex

EntireName: Cryo-EM structure of VcLmuACB complex
Components
  • Complex: Cryo-EM structure of VcLmuACB complex
    • 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 complex

SupramoleculeName: Cryo-EM structure of VcLmuACB complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 400 KDa

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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: 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 #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: Lamassu C

MacromoleculeName: Lamassu C / type: protein_or_peptide / ID: 3 / 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

Concentration1 mg/mL
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: 54.432 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1535228
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.70) / Number images used: 122532
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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