[English] 日本語
Yorodumi
- EMDB-64575: CryoEM Structure of LmuAB-DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64575
TitleCryoEM Structure of LmuAB-DNA complex
Map dataCryoEM map of LmuAB-DNA complex
Sample
  • Complex: CryoEM structure of LmuAB-DNA complex
    • Protein or peptide: Lamassu protein LmuB
    • Protein or peptide: Lamassu protein LmuA
    • DNA: DNA (41-MER)
  • DNA: DNA (41-MER)
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) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.73 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

-
Structure visualization

Supplemental images

emd_64575.png

Downloads & links

-
Map

FileDownload / File: emd_64575.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of LmuAB-DNA complex
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: 0.035
Minimum - Maximum-0.6208606 - 0.9016756
Average (Standard dev.)0.00006336402 (±0.016112838)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Additional map: CryoEM map of LmuAB-DNA complex

Fileemd_64575_additional_1.map
AnnotationCryoEM map of LmuAB-DNA complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: CryoEM half map of LmuAB-DNA complex

Fileemd_64575_half_map_1.map
AnnotationCryoEM half map of LmuAB-DNA complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: CryoEM half map of LmuAB-DNA complex

Fileemd_64575_half_map_2.map
AnnotationCryoEM half map of LmuAB-DNA complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CryoEM structure of LmuAB-DNA complex

EntireName: CryoEM structure of LmuAB-DNA complex
Components
  • Complex: CryoEM structure of LmuAB-DNA complex
    • Protein or peptide: Lamassu protein LmuB
    • Protein or peptide: Lamassu protein LmuA
    • DNA: DNA (41-MER)
  • DNA: DNA (41-MER)

-
Supramolecule #1: CryoEM structure of LmuAB-DNA complex

SupramoleculeName: CryoEM structure of LmuAB-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2, #4
Source (natural)Organism: Bacillus sp. (strain NCIM 5461 / CCTCC AB 2011126 / NIO-1130) (bacteria)
Molecular weightTheoretical: 180 KDa

-
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

-
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

-
Macromolecule #3: DNA (41-MER)

MacromoleculeName: DNA (41-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.594122 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)

-
Macromolecule #4: DNA (41-MER)

MacromoleculeName: DNA (41-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.647128 KDa
SequenceString:
(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)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5.0 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.4 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

+
Image processing

Particle selectionNumber selected: 1144023
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 437756
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more