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- EMDB-64586: type II Lamassu, LmuACB from Vibrio cholerae O1 El -

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Basic information

Entry
Database: EMDB / ID: EMD-64586
Titletype II Lamassu, LmuACB from Vibrio cholerae O1 El
Map data
Sample
  • Complex: Cryo-EM structure of VcLmuACB complex
    • Protein or peptide: DUF3732 domain-containing protein
    • Protein or peptide: Lamassu C
    • Protein or peptide: ABC-three component systems C-terminal domain-containing protein
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: 4.07 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_64586.png

Downloads & links

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Map

FileDownload / File: emd_64586.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 Å		0.82 Å/pix.
x 512 pix.
= 419.84 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: 0.003
Minimum - Maximum-0.032291014 - 0.106423736
Average (Standard dev.)0.000035019646 (±0.002347432)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_64586_additional_1.map
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Half map: #2

Fileemd_64586_half_map_1.map
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Half map: #1

Fileemd_64586_half_map_2.map
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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: Lamassu C
    • Protein or peptide: ABC-three component systems C-terminal domain-containing protein

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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: 210 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: 74.870195 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMFFQIEKV VLWSKEAKHK PRVIEFALNK VNLITGSSKS GKSSLIPIID YCLGSSKCSI PVNTIRDTTA WYGVQIKTKH SRLLIARRD PSNQLSTSNA FFVEAENIEI PQNIEKHNVN IDTVKNRLNE ISGVSNISFD FYDTGRIDKK RTSTRDLSAF N YQPQNIIA ...String:
GSMFFQIEKV VLWSKEAKHK PRVIEFALNK VNLITGSSKS GKSSLIPIID YCLGSSKCSI PVNTIRDTTA WYGVQIKTKH SRLLIARRD PSNQLSTSNA FFVEAENIEI PQNIEKHNVN IDTVKNRLNE ISGVSNISFD FYDTGRIDKK RTSTRDLSAF N YQPQNIIA NPNALFYKTD SFEHKSKLVT ILPYVLGALS NTDIENQHRI KNLEEEYRKV ERRLLKLKRQ NEDWLSSAQA YV IKAMELG LVNSDKDIYQ LKPERLLNVL KNIATKEIDY STSAANIKYA SEQEAEITKR SRDISNNLAK VKSRLQNINS MNR LANTHS DASRLKRERL SLSKWLLTQN DINSSLFSEP NEIRSLVLEP LARAFSNLEA ELEVPIHVQG ALSREKIYLE GELT RLASE MKDVNTQLKI LRGNKRKLGY DAFSVGKFVG EVEKALSLMG ESESESELSK EYKRLKKELS VLRLKIDPRE FERKT KLQL AKVNKLASDW LPHLDTENPN APISLHEKEL TITVNSSGRE DYLWEIGSGA NWLSYHVAIT LALHQHFSSL EASPVP NYI IYDQPSQVYF PSKLRHQATP EEDELALLEQ DEDIVQVKKI FEAFNGAIEK TKDNLQIIVL DHAPSTLVKS IPKGHLV EE WRNGIKLIPL DWL

UniProtKB: DUF3732 domain-containing protein

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Macromolecule #2: Lamassu C

MacromoleculeName: Lamassu C / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio cholerae (bacteria)
Molecular weightTheoretical: 19.483674 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSMLKPENNL EKEAWEINNP AMCSYMLWIA TLAYYQKQKE PIHPSRLFCL FPFILYSDTR NVLLSSKGSL KSYLAKFSNS KAISGDIPL SIHFRIDIQK NKTLDALIVA FDSGLLVIDS DSGLIKPNVS IKPLPNSKLT DTIKELVYCS TKIGRWLSEM T NQDLARDL KVIF

UniProtKB: Uncharacterized protein

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Macromolecule #3: ABC-three component systems C-terminal domain-containing protein

MacromoleculeName: ABC-three component systems C-terminal domain-containing protein
type: protein_or_peptide / ID: 3 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.83 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: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10027902
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.70) / Number images used: 78853
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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