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- EMDB-65215: Bacillus Subtilis Ku core homodimer complexed with double strand DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-65215
TitleBacillus Subtilis Ku core homodimer complexed with double strand DNA
Map data
Sample
  • Complex: Bacillus Subtilis Ku core homodimer complexed with double strand DNA
    • Protein or peptide: Non-homologous end joining protein Ku
    • DNA: DNA (31-MER)
    • DNA: DNA (31-MER)
KeywordsNon homologous end joining / DNA bridging / DNA BINDING PROTEIN
Function / homologyNon-homologous end joining protein Ku, prokaryotic type / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / double-strand break repair via nonhomologous end joining / double-stranded DNA binding / DNA recombination / Non-homologous end joining protein Ku
Function and homology information
Biological speciesBacillus subtilis (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsKim WJ / Kim MS
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structure of Bacillus subtilis Ku-mediated DNA synaptic complex.
Authors: Whan-Jong Kim / Jieun Kim / Mingyu Jo / Youngjin Kim / Min-Sung Kim /
Abstract: DNA double-strand breaks (DSBs) pose a severe threat to genomic integrity, and cells rely on two major pathways for repair: homologous recombination and non-homologous end joining (NHEJ). While ...DNA double-strand breaks (DSBs) pose a severe threat to genomic integrity, and cells rely on two major pathways for repair: homologous recombination and non-homologous end joining (NHEJ). While eukaryotic NHEJ requires a multi-component assembly including the Ku70/80 heterodimer, bacterial NHEJ operates with a simpler toolkit comprising a Ku homodimer and the multifunctional LigD. Despite this simplicity, the mechanism by which broken DNA ends are bridged together has remained unclear in bacterial NHEJ. Here, we present a cryo-electron microscopy structure of the Bacillus subtilis Ku (bsKu)-DNA complex at 2.74 Å resolution, capturing two blunt DNA ends bridged by a Ku protein alone. Supported by further biochemical assays, we propose an integrated model in which oligomeric arrays of Ku homodimers bridge and stabilize two DNA ends, facilitating efficient DSB repair in Bacillus subtilis. This work reveals a bsKu-mediated DNA bridging mechanism distinct from the eukaryotic system and provides critical structural insight into prokaryotic DNA repair.
History
DepositionJun 30, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_65215.png

Downloads & links

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Map

FileDownload / File: emd_65215.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 400 pix.
= 329.92 Å		0.82 Å/pix.
x 400 pix.
= 329.92 Å		0.82 Å/pix.
x 400 pix.
= 329.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8248 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.066
Minimum - Maximum-0.3744026 - 0.6676028
Average (Standard dev.)-0.000078022334 (±0.012054259)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 329.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65215_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_65215_half_map_2.map
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Sample components

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Entire : Bacillus Subtilis Ku core homodimer complexed with double strand DNA

EntireName: Bacillus Subtilis Ku core homodimer complexed with double strand DNA
Components
  • Complex: Bacillus Subtilis Ku core homodimer complexed with double strand DNA
    • Protein or peptide: Non-homologous end joining protein Ku
    • DNA: DNA (31-MER)
    • DNA: DNA (31-MER)

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Supramolecule #1: Bacillus Subtilis Ku core homodimer complexed with double strand DNA

SupramoleculeName: Bacillus Subtilis Ku core homodimer complexed with double strand DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bacillus subtilis (bacteria)

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Macromolecule #1: Non-homologous end joining protein Ku

MacromoleculeName: Non-homologous end joining protein Ku / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bacillus subtilis (bacteria)
Molecular weightTheoretical: 26.052652 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHTMWKGSIS FGLVNIPIKL YAATEDKDIK LRSLHKEDHA PIKYEKVCTN CEKTLSPDEI VKGYEYVKGK YVVLTDEDLK SLKQEHEEK AVEIVDFVQL QEIDPIYFNR SYFVGPGDNG TKAYTLLREA LRSTGKIGIA NMTIRSKQQL AILRVYENCI V MESIHYPD ...String:
MHTMWKGSIS FGLVNIPIKL YAATEDKDIK LRSLHKEDHA PIKYEKVCTN CEKTLSPDEI VKGYEYVKGK YVVLTDEDLK SLKQEHEEK AVEIVDFVQL QEIDPIYFNR SYFVGPGDNG TKAYTLLREA LRSTGKIGIA NMTIRSKQQL AILRVYENCI V MESIHYPD EVRSAAQVPG VPDQSNVNDK ELQTAITLID ELTAKFEPEK YEDTYRQALL QRVNDKLEN

UniProtKB: Non-homologous end joining protein Ku

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Macromolecule #2: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.616208 KDa
SequenceString:
(DC)(DT)(DG)(DT)(DA)(DG)(DA)(DA)(DG)(DG) (DT)(DA)(DC)(DC)(DT)(DG)(DT)(DA)(DG)(DA) (DA)(DG)(DG)(DT)(DA)(DC)(DC)(DT)(DG) (DT)(DA)

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Macromolecule #3: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.447097 KDa
SequenceString:
(DT)(DA)(DC)(DA)(DG)(DG)(DT)(DA)(DC)(DC) (DT)(DT)(DC)(DT)(DA)(DC)(DA)(DG)(DG)(DT) (DA)(DC)(DC)(DT)(DT)(DC)(DT)(DA)(DC) (DA)(DG)

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 156247
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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