[English] 日本語
Yorodumi
- EMDB-52347: Salmonella enterica Lamassu LmuACB in nuclease sequestration state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52347
TitleSalmonella enterica Lamassu LmuACB in nuclease sequestration state
Map data
Sample
  • Complex: LmuACB
    • Protein or peptide: DUF3732 domain-containing protein
    • Protein or peptide: ABC-three component systems C-terminal domain-containing protein
    • Protein or peptide: LmuC
KeywordsLamassu / Rad50 / Cap4 / bacterial immunity / defence system / DNA end binding / ABC ATPase / SMC-like / Cap4 nuclease / phage / plasmid restriction / IMMUNE SYSTEM
Function / homology
Function and homology information


Protein 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DUF3732 domain-containing protein / ABC-three component systems C-terminal domain-containing protein / Uncharacterized protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Tennessee (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 Å
AuthorsLi Y / Gruber S
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation320030-227915 Switzerland
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structure and activation mechanism of a Lamassu phage and plasmid defense system.
Authors: Yan Li / David W Adams / Hon Wing Liu / Steven J Shaw / Emiko Uchikawa / Milena Jaskólska / Sandrine Stutzmann / Laurie Righi / Mark D Szczelkun / Melanie Blokesch / Stephan Gruber /
Abstract: Lamassu is a diverse family of defense systems that protect bacteria, including seventh-pandemic strains of Vibrio cholerae, against both plasmids and phage infection. During phage infection, Lamassu ...Lamassu is a diverse family of defense systems that protect bacteria, including seventh-pandemic strains of Vibrio cholerae, against both plasmids and phage infection. During phage infection, Lamassu targets essential cellular processes, thereby halting phage propagation by terminating the infected host. The mechanisms by which Lamassu effectors are activated when needed and otherwise suppressed are unknown. Here we present structures of a Lamassu defense system from Salmonella enterica. We show that an oligomerization domain of the nuclease effector subunit, LmuA, is sequestered by two tightly folded SMC-like LmuB protomers and LmuC. Upon activation, liberated LmuA assembles into homotetramers, in which two of four nuclease domains are brought into proximity to create an active site capable of cleaving DNA. We propose that tetramer formation is likely a one-way switch that establishes a threshold to limit potential spontaneous activation and cell death. Our findings reveal a mechanism of cellular defense, involving liberation and oligomerization of immune effectors, and shed light on how Lamassu systems balance potent immune responses with self-preservation.
History
DepositionDec 17, 2024-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateDec 24, 2025-
Current statusDec 24, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52347.png

Downloads & links

-
Map

FileDownload / File: emd_52347.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 350 pix.
= 290.5 Å		0.83 Å/pix.
x 350 pix.
= 290.5 Å		0.83 Å/pix.
x 350 pix.
= 290.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0691
Minimum - Maximum-0.6824419 - 0.90953267
Average (Standard dev.)0.00009169819 (±0.01572237)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 290.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_52347_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_52347_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_52347_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : LmuACB

EntireName: LmuACB
Components
  • Complex: LmuACB
    • Protein or peptide: DUF3732 domain-containing protein
    • Protein or peptide: ABC-three component systems C-terminal domain-containing protein
    • Protein or peptide: LmuC

-
Supramolecule #1: LmuACB

SupramoleculeName: LmuACB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Tennessee (bacteria)
Strain: TXSC_TXSC08-19

-
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: Salmonella enterica subsp. enterica serovar Tennessee (bacteria)
Strain: TXSC_TXSC08-19
Molecular weightTheoretical: 75.235875 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYFQIRGIIL WPRNKNFKPH TIRFELGKVN VISGASRTGK SAVIPIIDYC LGANTCSIPV KTIRKYCEWF GIVVATEQGE KLLARKEPG NQRSTTDMFV LEAENITSIP IRLEKNTNVI AVKRMLDDLA NLSNLDFSGG DENSGFDGRP AFRDLAAFTF Q PQNVVANP ...String:
MYFQIRGIIL WPRNKNFKPH TIRFELGKVN VISGASRTGK SAVIPIIDYC LGANTCSIPV KTIRKYCEWF GIVVATEQGE KLLARKEPG NQRSTTDMFV LEAENITSIP IRLEKNTNVI AVKRMLDDLA NLSNLDFSGG DENSGFDGRP AFRDLAAFTF Q PQNVVANP DVLFFKTNTY EHREKLRKIF PYVLGAITSE LMAKQFELNR IRLFLRRKER ELKDAQDVSA QWLADLKSKY SE AQELGLV PKPQEQLSRK QMISQLEEVI SRTDLTLKVT VSTISDALSE LNTLESEERL VSRELTTMRH RLEEMNRLRV GMH QYENAL LMQRDRLKIS GWLLSNTNDE SDCPMCGSHT DSAKQKLQAL VQRLSDVEAA VGADAHKEVP AAFDRELQRV TTEV ANATE RLRAIQSRKR TLTSRSKEAR EQQFSTRRAE RFIGNVESAL ELHRKLGSDS ELVEEVRKLK EMVQTLEKEL REKDV ELRK NQALRVINAQ AGNILQGLDV EDPSAPISLE INDLTIKVLG DERDDYLSEI GSGSNWLSYH LAILLSLHQF YLSQKN NPV PSFLILDQPS QVYFPKTTQL PNIANEDEPK LRDEDVEAVR RAFKAMGNVV IKEKGKLQLI VLDHAPREVW GEIDGVV GL PEWRDGIKLV PMEWLTGV

UniProtKB: DUF3732 domain-containing protein

-
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: Salmonella enterica subsp. enterica serovar Tennessee (bacteria)
Strain: TXSC_TXSC08-19
Molecular weightTheoretical: 45.38141 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAISKTNGQS KPKRKTEVPG QALGYSLQFT LLTHLLLQAP EGSLCSLEVL DDVAQENNSG DIKFIQSKSA LTANPAADRA KSLWKTLSN WIDLATSPDF EVEKAIFELY VSRPVEGSIV KKFNEAKTPE DAQEAITHAR TELWGDSPHF TLKDGISKEI S KYVEKVFT ...String:
MAISKTNGQS KPKRKTEVPG QALGYSLQFT LLTHLLLQAP EGSLCSLEVL DDVAQENNSG DIKFIQSKSA LTANPAADRA KSLWKTLSN WIDLATSPDF EVEKAIFELY VSRPVEGSIV KKFNEAKTPE DAQEAITHAR TELWGDSPHF TLKDGISKEI S KYVEKVFT ADQNLLQRLI CNFQLTLGSG SPQADLEACV RSHPVSPSKV SDITNYLCGK VKRHIDMLLE AEKPAVIARD DF YTWYKAY VQKIDRQMVL SSRAQAPVKE KAQEYLPDKF VQQLEIIGLP YEEILGAISD YLMASFDRTD WAARGEVDET SFD DLDTAL QRTWKNKQRI CGLTHSEKSE QDQGKLLYFE CMQFNIPLQA MSPPSHFIPG CYHILADSLA VGWHPNYTTQ LKNK KVA

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

-
Macromolecule #3: LmuC

MacromoleculeName: LmuC / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Tennessee (bacteria)
Strain: TXSC_TXSC08-19
Molecular weightTheoretical: 18.377428 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLAREAQNIQ NPALGAALVW RFCCGYVKTN RVSAPPPLPF LFLVLPIILH QETSEFVKRT YKSSGLRAFA AKFGDSSVSK QDLLFQIHE RSIRWRQLSL RSIELAVASD LLKLQDGSDV IPLSKTKARG LSDEVKTLMD LAEKLGSWFG ELSIHEVVTT L KVKL

UniProtKB: Uncharacterized protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

-
Sample preparation

BufferpH: 7.5 / Component - Concentration: 150.0 mM / Component - Formula: NaCl / Component - Name: Sodium Chloride
Details: 150 mM NaCl, 20mM HEPES, pH7.5, 1mM Tcep, 5mM MgCl2, 1mM ATP, 0.05% b-OG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 242023
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9hqu:
Salmonella enterica Lamassu LmuACB in nuclease sequestration state

+
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