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- EMDB-42978: CryoEM structure of Ku homodimer in complex with hairpin DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-42978
TitleCryoEM structure of Ku homodimer in complex with hairpin DNA
Map dataDensity modified and masked map: Generated by boxing and density modification in Phenix(Resolve cryoEM) Unmasked density modified map is provided in additional EM map section.
Sample
  • Complex: Ku homodimer from M.tubeculosis in complex with hairpin DNA
    • DNA: DNA (21-MER)
    • DNA: DNA (34-MER)
    • Protein or peptide: Non-homologous end joining protein Ku
KeywordsNHEJ / DNA repair / Mycobacterium tuberculosis / DNA synapsis / 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 H37Rv (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsBaral J / Rouiller I / Das AK
Funding support Australia, India, 2 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2000934 Australia
Science and Engineering Research Board (SERB)CRG/2020/002622 India
CitationJournal: To Be Published
Title: First cryoEM structure of bacterial Ku in complex with DNA
Authors: Baral J / Rouiller I / Das AK
History
DepositionNov 30, 2023-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42978.png

Downloads & links

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Map

FileDownload / File: emd_42978.map.gz / Format: CCP4 / Size: 2.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity modified and masked map: Generated by boxing and density modification in Phenix(Resolve cryoEM) Unmasked density modified map is provided in additional EM map section.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 94 pix.
= 78.302 Å		0.83 Å/pix.
x 84 pix.
= 69.972 Å		0.83 Å/pix.
x 88 pix.
= 73.304 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-11.579405 - 13.180294
Average (Standard dev.)-0.038185064 (±1.143142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin214213190
Dimensions848894
Spacing888494
CellA: 73.304 Å / B: 69.972 Å / C: 78.302 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42978_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Raw map: Generated from Cryosparc (Non-uniform refinement).

Fileemd_42978_additional_1.map
AnnotationRaw map: Generated from Cryosparc (Non-uniform refinement).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Density modified map: Generated by boxing and density...

Fileemd_42978_additional_2.map
AnnotationDensity modified map: Generated by boxing and density modification in Phenix(Resolve cryoEM)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Raw half map A: Generated from Cryosparc (Non-uniform refinement).

Fileemd_42978_half_map_1.map
AnnotationRaw half map A: Generated from Cryosparc (Non-uniform refinement).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Raw half map B: Generated from Cryosparc (Non-uniform refinement).

Fileemd_42978_half_map_2.map
AnnotationRaw half map B: Generated from Cryosparc (Non-uniform refinement).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ku homodimer from M.tubeculosis in complex with hairpin DNA

EntireName: Ku homodimer from M.tubeculosis in complex with hairpin DNA
Components
  • Complex: Ku homodimer from M.tubeculosis in complex with hairpin DNA
    • DNA: DNA (21-MER)
    • DNA: DNA (34-MER)
    • Protein or peptide: Non-homologous end joining protein Ku

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Supramolecule #1: Ku homodimer from M.tubeculosis in complex with hairpin DNA

SupramoleculeName: Ku homodimer from M.tubeculosis in complex with hairpin DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #1
Details: Protein: Ku homodimer was recombination purified DNA: Chemically Synthesized
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (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: 2 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 33.609898 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGHHHHHHHH HHSSGHIEGR HMMRAIWTGS IAFGLVNVPV KVYSATADHD IRFHQVHAKD NGRIRYKRVC EACGEVVDYR DLARAYESG DGQMVAITDD DIASLPEERS REIEVLEFVP AADVDPMMFD RSYFLEPDSK SSKSYVLLAK TLAETDRMAI V HFTLRNKT ...String:
MGHHHHHHHH HHSSGHIEGR HMMRAIWTGS IAFGLVNVPV KVYSATADHD IRFHQVHAKD NGRIRYKRVC EACGEVVDYR DLARAYESG DGQMVAITDD DIASLPEERS REIEVLEFVP AADVDPMMFD RSYFLEPDSK SSKSYVLLAK TLAETDRMAI V HFTLRNKT RLAALRVKDF GKREVMMVHT LLWPDEIRDP DFPVLDQKVE IKPAELKMAG QVVDSMADDF NPDRYHDTYQ EQ LQELIDT KLEGGQAFTA EDQPRLLDEP EDVSDLLAKL EASVKARSKA NSNVPTPP

UniProtKB: Non-homologous end joining protein Ku

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Macromolecule #2: DNA (21-MER)

MacromoleculeName: DNA (21-MER) / type: dna / ID: 2 / Details: Sequence was obtained from PDB:1JEY / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.506188 KDa
SequenceString:
(DG)(DT)(DT)(DT)(DT)(DT)(DA)(DG)(DT)(DT) (DT)(DA)(DT)(DT)(DG)(DG)(DG)(DC)(DG)(DC) (DG)

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Macromolecule #3: DNA (34-MER)

MacromoleculeName: DNA (34-MER) / type: dna / ID: 3 / Details: Sequence was obtained from PDB:1JEY / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.325685 KDa
SequenceString:
(DC)(DG)(DC)(DG)(DC)(DC)(DC)(DA)(DG)(DC) (DT)(DT)(DT)(DC)(DC)(DC)(DA)(DG)(DC)(DT) (DA)(DA)(DT)(DA)(DA)(DA)(DC)(DT)(DA) (DA)(DA)(DA)(DA)(DC)

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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

Concentration0.17 mg/mL
BufferpH: 7.5
Component:
ConcentrationName
50.0 mMHEPES (4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid)
150.0 mMSodium chloride
2.0 mMTris(2-carboxyethyl)phosphine hydrochloride

Details: 50mM HEPES, 150mM NaCl, 2mM TCEP
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6151 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5291688
CTF correctionSoftware - Name: cryoSPARC / Details: Peformed in CryoSPARC Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Alphafold ID: AF-P9WKD9-F1
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: OTHER / Software - Name: cryoSPARC / Details: Mean resolution obtained from ResMap: 3.4 / Number images used: 110000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9-f1


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8v53:
CryoEM structure of Ku homodimer in complex with hairpin DNA

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