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- EMDB-52748: Ku from Mycobacterium tuberculosis bound to DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-52748
TitleKu from Mycobacterium tuberculosis bound to DNA
Map data
Sample
  • Complex: KuTB-DNA complex
    • Protein or peptide: Non-homologous end joining protein Ku
    • DNA: DNA 1
    • DNA: DNA 2
  • Ligand: water
KeywordsDNA repair / tuberculosis / NHEJ / DNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of ligase activity / DNA helicase complex / double-strand break repair via nonhomologous end joining / double-stranded DNA binding / DNA recombination / protein homodimerization activity
Similarity search - Function
Non-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
Similarity search - Domain/homology
Non-homologous end joining protein Ku
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria) / DNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsChaplin AK / Zahid S
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/X00029X/1 United Kingdom
The Lister Institute of Preventive Medicine United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Oligomerisation of Ku from Mycobacterium tuberculosis promotes DNA synapsis.
Authors: Sayma Zahid / Sonia Baconnais / Henrietta Smith / Saseela Atwal / Lucy Bates / Harriet Read / Ankita Chadda / Florian Morati / Tom Bedwell / Emil G P Stender / Joanne Walter / Steven W ...Authors: Sayma Zahid / Sonia Baconnais / Henrietta Smith / Saseela Atwal / Lucy Bates / Harriet Read / Ankita Chadda / Florian Morati / Tom Bedwell / Emil G P Stender / Joanne Walter / Steven W Hardwick / Fredrik Westerlund / Eric Galburt / Eric Le Cam / Alice Pyne / Galina V Mukamolova / Amanda K Chaplin /
Abstract: Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is estimated to infect nearly one-quarter of the global population. A key factor in its resilience and persistence is its ...Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), is estimated to infect nearly one-quarter of the global population. A key factor in its resilience and persistence is its robust DNA repair capacity. Non-homologous end joining (NHEJ) is the primary pathway for repairing DNA double-strand breaks (DSBs) in many organisms, including Mtb, where it is mediated by the Ku protein and the multifunctional LigD enzyme. In this study, we demonstrate that Ku is essential for mycobacterial survival under DNA-damaging conditions. Using cryogenic electron microscopy (cryo-EM), we solved high-resolution structures of both the apo and DNA-bound forms of the Ku-Mtb homodimer. Our structural and biophysical analyses reveal that Ku forms an extended proteo-filament upon binding DNA. We identify critical residues involved in filament formation and DNA synapsis and show that their mutation severely impairs bacterial viability. Furthermore, we propose a model in which the C-terminus of Ku regulates DNA binding and loading and facilitates subsequent recruitment of LigD. These findings provide unique insights into bacterial DNA repair and guide future therapeutics.
History
DepositionFeb 6, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52748.png

Downloads & links

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Map

FileDownload / File: emd_52748.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.82 Å/pix.
x 416 pix.
= 342.784 Å		0.82 Å/pix.
x 416 pix.
= 342.784 Å		0.82 Å/pix.
x 416 pix.
= 342.784 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.038
Minimum - Maximum-0.15557058 - 0.33760723
Average (Standard dev.)0.00015311813 (±0.006040007)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 342.784 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52748_msk_1.map
Projections & Slices
AxesZYX

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Additional map: locally refined composite map

Fileemd_52748_additional_1.map
Annotationlocally refined composite map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_52748_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_52748_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : KuTB-DNA complex

EntireName: KuTB-DNA complex
Components
  • Complex: KuTB-DNA complex
    • Protein or peptide: Non-homologous end joining protein Ku
    • DNA: DNA 1
    • DNA: DNA 2
  • Ligand: water

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Supramolecule #1: KuTB-DNA complex

SupramoleculeName: KuTB-DNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Mycobacterium tuberculosis (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: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 33.47757 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAHHHHHHVG TGSNDDDDKS PDPMRAIWTG SIAFGLVNVP VKVYSATADH DIRFHQVHAK DNGRIRYKRV CEACGEVVDY RDLARAYES GDGQMVAITD DDIASLPEER SREIEVLEFV PAADVDPMMF DRSYFLEPDS KSSKSYVLLA KTLAETDRMA I VHFTLRNK ...String:
MAHHHHHHVG TGSNDDDDKS PDPMRAIWTG SIAFGLVNVP VKVYSATADH DIRFHQVHAK DNGRIRYKRV CEACGEVVDY RDLARAYES GDGQMVAITD DDIASLPEER SREIEVLEFV PAADVDPMMF DRSYFLEPDS KSSKSYVLLA KTLAETDRMA I VHFTLRNK TRLAALRVKD FGKREVMMVH TLLWPDEIRD PDFPVLDQKV EIKPAELKMA GQVVDSMADD FNPDRYHDTY QE QLQELID TKLEGGQAFT AEDQPRLLDE PEDVSDLLAK LEASVKARSK ANSNVPTPP

UniProtKB: Non-homologous end joining protein Ku

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Macromolecule #2: DNA 1

MacromoleculeName: DNA 1 / type: dna / ID: 2 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 9.947389 KDa
SequenceString:
(DG)(DG)(DA)(DA)(DT)(DG)(DT)(DA)(DA)(DC) (DC)(DA)(DT)(DC)(DG)(DT)(DT)(DG)(DG)(DT) (DC)(DG)(DG)(DC)(DA)(DG)(DC)(DA)(DG) (DG)(DG)(DC)

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Macromolecule #3: DNA 2

MacromoleculeName: DNA 2 / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 9.738257 KDa
SequenceString:
(DG)(DC)(DC)(DC)(DT)(DG)(DC)(DT)(DG)(DC) (DC)(DG)(DA)(DC)(DC)(DA)(DA)(DC)(DG)(DA) (DT)(DG)(DG)(DT)(DT)(DA)(DC)(DA)(DT) (DT)(DC)(DC)

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
Component:
ConcentrationFormulaName
20.0 mMTris-HClTris-HCl
75.0 mMNaClSodium Chloride
5.0 mMMgCl2Magnesium Chloride
2.0 mMDTTDithiothreitol
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 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: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 147904
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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