[English] 日本語
Yorodumi
- EMDB-49911: LmuA_conformation 1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49911
TitleLmuA_conformation 1
Map dataLmuA_conformation 1
Sample
  • Cell: LmuA_symmetric conformation
    • Protein or peptide: ABC-three component systems C-terminal domain-containing protein
KeywordsLmuA-conformation 1 / DNA BINDING PROTEIN
Function / homologyABC-three component systems, C-terminal domain 7 / C-terminal domain 7 of the ABC-three component (ABC-3C) systems / ABC-three component systems C-terminal domain-containing protein
Function and homology information
Biological speciesEscherichia coli (E. coli) / Vibrio cholerae (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 Å
AuthorsChakravarti A / Zhang Z
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structural basis for Lamassu-based antiviral immunity and its evolution from DNA repair machinery.
Authors: Matthieu Haudiquet / Arpita Chakravarti / Zhiying Zhang / Josephine L Ramirez / Alba Herrero Del Valle / Paul Dominic B Olinares / Rachel Lavenir / Massilia Aït Ahmed / M Jason de la Cruz / ...Authors: Matthieu Haudiquet / Arpita Chakravarti / Zhiying Zhang / Josephine L Ramirez / Alba Herrero Del Valle / Paul Dominic B Olinares / Rachel Lavenir / Massilia Aït Ahmed / M Jason de la Cruz / Brian T Chait / Samuel H Sternberg / Aude Bernheim / Dinshaw J Patel /
Abstract: Bacterial immune systems exhibit remarkable diversity and modularity, as a consequence of the continuous selective pressures imposed by phage predation. Despite recent mechanistic advances, the ...Bacterial immune systems exhibit remarkable diversity and modularity, as a consequence of the continuous selective pressures imposed by phage predation. Despite recent mechanistic advances, the evolutionary origins of many antiphage immune systems remain elusive, especially for those that encode homologs of the structural maintenance of chromosomes (SMC) superfamily, which are essential for chromosome maintenance and DNA repair across domains of life. Here, we elucidate the structural basis and evolutionary emergence of Lamassu, a bacterial immune system family featuring diverse effectors but a core conserved SMC-like sensor. Using cryo-EM, we determined structures of the Lamassu complex in both apo- and dsDNA-bound states, revealing unexpected stoichiometry and topological architectures. We further demonstrate how Lamassu specifically senses dsDNA ends in vitro and phage replication origins in vivo, thereby triggering the formation of LmuA tetramers that activate its Cap4 nuclease domain. Our findings reveal that Lamassu evolved via exaptation of the bacterial Rad50-Mre11 DNA repair system to form a compact, modular sensor for viral replication, exemplifying how cellular machinery can be co-opted for novel immune functions.
History
DepositionMar 26, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49911.png

Downloads & links

-
Map

FileDownload / File: emd_49911.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLmuA_conformation 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 340.48 Å		1.06 Å/pix.
x 320 pix.
= 340.48 Å		1.06 Å/pix.
x 320 pix.
= 340.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.064 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.168
Minimum - Maximum-2.1065087 - 3.1465242
Average (Standard dev.)-0.0001625471 (±0.044475622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 340.48 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map B

Fileemd_49911_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map A

Fileemd_49911_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : LmuA_symmetric conformation

EntireName: LmuA_symmetric conformation
Components
  • Cell: LmuA_symmetric conformation
    • Protein or peptide: ABC-three component systems C-terminal domain-containing protein

-
Supramolecule #1: LmuA_symmetric conformation

SupramoleculeName: LmuA_symmetric conformation / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

-
Macromolecule #1: ABC-three component systems C-terminal domain-containing protein

MacromoleculeName: ABC-three component systems C-terminal domain-containing protein
type: protein_or_peptide / ID: 1 / Number of copies: 4 / 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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 193953
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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