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- EMDB-64576: CryoEM Structure of LmuAB Apo State -

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Basic information

Entry
Database: EMDB / ID: EMD-64576
TitleCryoEM Structure of LmuAB Apo State
Map dataCryoEM map of LmuAB Apo state
Sample
  • Complex: CryoEM structure of LmuAB-Apo State
    • Protein or peptide: Lamassu protein LmuB
    • Protein or peptide: Lamassu protein LmuA
Keywordscomplex / anti-phage system / IMMUNE SYSTEM
Function / homologyCD-NTase associated protein 4, DNA endonuclease domain / Cap4, dsDNA endonuclease domain / nuclease activity / defense response to virus / hydrolase activity / P-loop containing nucleoside triphosphate hydrolase / Lamassu protein LmuA / Lamassu protein LmuB
Function and homology information
Biological speciesBacillus sp. (strain NCIM 5461 / CCTCC AB 2011126 / NIO-1130) (bacteria) / Bacillus sp. nio-1130 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsLi M / Zhao X / An L / Li S / Zhang K / Feng Y / Chang C
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 13, 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_64576.png

Downloads & links

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Map

FileDownload / File: emd_64576.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of LmuAB Apo state
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: 0.05
Minimum - Maximum-0.6848657 - 1.0453131
Average (Standard dev.)0.0000224518 (±0.017735176)
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: CryoEM map of LmuAB Apo state

Fileemd_64576_additional_1.map
AnnotationCryoEM map of LmuAB Apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM half map of LmuAB Apo state

Fileemd_64576_half_map_1.map
AnnotationCryoEM half map of LmuAB Apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM half map of LmuAB Apo state

Fileemd_64576_half_map_2.map
AnnotationCryoEM half map of LmuAB Apo state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CryoEM structure of LmuAB-Apo State

EntireName: CryoEM structure of LmuAB-Apo State
Components
  • Complex: CryoEM structure of LmuAB-Apo State
    • Protein or peptide: Lamassu protein LmuB
    • Protein or peptide: Lamassu protein LmuA

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Supramolecule #1: CryoEM structure of LmuAB-Apo State

SupramoleculeName: CryoEM structure of LmuAB-Apo State / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus sp. (strain NCIM 5461 / CCTCC AB 2011126 / NIO-1130) (bacteria)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: Lamassu protein LmuB

MacromoleculeName: Lamassu protein LmuB / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. nio-1130 (bacteria)
Molecular weightTheoretical: 66.507977 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIIIAFSILD FKNKEAQNFD FKAGTNLIVS KGNTKGKSSL LKSMYYTLGF DVHQFPSNWN INFMYFQIEV LINNVKYNIT RQKNIFRVS DVEVPLNVKE YSEWLQHKLE IKMQLANTHT KHLYEAYSSA VILPFYIDQD DSWDGGIYRN VTNTLNQYTR I PADIFKSV ...String:
MIIIAFSILD FKNKEAQNFD FKAGTNLIVS KGNTKGKSSL LKSMYYTLGF DVHQFPSNWN INFMYFQIEV LINNVKYNIT RQKNIFRVS DVEVPLNVKE YSEWLQHKLE IKMQLANTHT KHLYEAYSSA VILPFYIDQD DSWDGGIYRN VTNTLNQYTR I PADIFKSV FNLSNYELLE LQNSLTNYSK EKNTVVSTIK SLLNVLEDYR HENADVPTVS KIDKIALNKD IDRYLQMQNE LN EQIVKYK MKLLNKQEML DLQKQELSEL EQLLKMNKKR YNSIETECQY CHSKLTKEQS LTRLDLSNNY FEISLLKEEI EKE VVKLTN EIIIFESQQN SIESKIDEIH RRIQNSKDLL TIDDYVKATA KKEASNELES LVDKQVLSKY NLEEKIKVLR REIN KLKKE KESLREIIER DYTDLVFEIK KVLNDLNDTK LDLSELNLDE LKFLEFKKIS GSGMDKNKKF LAYYLIYFSL LRKYS SYII PFCMDSFIKN EITGETAKKM FEAIEKYFFD TNQSFFSIVS ENLKHLEFVD SYNKINVEGK LLVRDKYDEI ALKFKF DS

UniProtKB: Lamassu protein LmuB

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Macromolecule #2: Lamassu protein LmuA

MacromoleculeName: Lamassu protein LmuA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. nio-1130 (bacteria)
Molecular weightTheoretical: 36.103793 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIEIDNGGAI ALKGFNYQKA SIILVMIHNF EKDNFIVIPE SQEDFEIHLG QDTYFIQVKG TKKLSIGKLK SRPSGKASII EKNLSPGNV GDIRKIFLWD IAELTKNELI SQEGTLIPMK HSLSLKQKTE IINTLDLDEE QKNRMNNQYI YITPFPNDIN L ALTFLKGE ...String:
MIEIDNGGAI ALKGFNYQKA SIILVMIHNF EKDNFIVIPE SQEDFEIHLG QDTYFIQVKG TKKLSIGKLK SRPSGKASII EKNLSPGNV GDIRKIFLWD IAELTKNELI SQEGTLIPMK HSLSLKQKTE IINTLDLDEE QKNRMNNQYI YITPFPNDIN L ALTFLKGE MVNENLLVSN DRAKLVLGEL SLEIDRKSEI VVSTESDVER KKIDGNYLKQ VFINIKQKEM FDEILDNLSI NT IMKKKVK KEKLRIPLLY QNIKEQTKQK ADINLLMREN DEGAINYLRD LLVEIVPDMK PTELSIALAI DCFCELGE

UniProtKB: Lamassu protein LmuA

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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

Concentration5.0 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: 52.5 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: 1.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1312792
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 447569
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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