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- EMDB-74422: CryoEM structure of Ku heterodimer bound to N7 nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-74422
TitleCryoEM structure of Ku heterodimer bound to N7 nucleosome
Map datacomplex of a Ku bound N7 nucleosome
Sample
  • Complex: Complex of Ku bound to Nucleosome with 7bp overhang
    • Complex: Nucleosome with 7bp overhang
      • DNA: DNA (154-mer)
      • DNA: DNA (154-mer)
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: Ku70/80
      • Protein or peptide: X-ray repair cross-complementing protein 6
      • Protein or peptide: X-ray repair cross-complementing protein 5
  • Ligand: water
KeywordsComplex / DNA repair / NHEJ / Nucleosome / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / cellular response to X-ray / regulation of smooth muscle cell proliferation ...Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / cellular response to X-ray / regulation of smooth muscle cell proliferation / double-strand break repair via classical nonhomologous end joining / Cytosolic sensors of pathogen-associated DNA / nuclear telomere cap complex / IRF3-mediated induction of type I IFN / cellular hyperosmotic salinity response / U3 snoRNA binding / regulation of telomere maintenance / recombinational repair / protein localization to chromosome, telomeric region / 2-LTR circle formation / telomeric repeat DNA binding / DNA 3'-5' helicase / 5'-deoxyribose-5-phosphate lyase activity / ATP-dependent activity, acting on DNA / 3'-5' DNA helicase activity / telomere maintenance via telomerase / activation of innate immune response / telomere maintenance / cyclin binding / DNA-(apurinic or apyrimidinic site) lyase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / site of DNA damage / double-strand break repair via nonhomologous end joining / small-subunit processome / Nonhomologous End-Joining (NHEJ) / cellular response to gamma radiation / protein-DNA complex / enzyme activator activity / nucleosomal DNA binding / innate immune response in mucosa / double-strand break repair / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / DNA recombination / antimicrobial humoral immune response mediated by antimicrobial peptide / double-stranded DNA binding / heterochromatin formation / scaffold protein binding / secretory granule lumen / transcription regulator complex / antibacterial humoral response / ficolin-1-rich granule lumen / innate immune response / damaged DNA binding / DNA helicase activity / chromosome, telomeric region / transcription cis-regulatory region binding / ribonucleoprotein complex / chromosome / protein heterodimerization activity / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / nucleolus / Neutrophil degranulation / positive regulation of DNA-templated transcription / protein-containing complex binding / DNA-templated transcription / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / protein-containing complex / DNA binding / RNA binding / nucleoplasm / ATP binding / extracellular region / membrane / nucleus / cytosol
Similarity search - Function
Ku70, bridge and pillars domain superfamily / : / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta ...Ku70, bridge and pillars domain superfamily / : / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / 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 / SAP domain superfamily / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / : / Histone H2B signature. / Histone H2B / Histone H2B / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
Histone H2B / Histone H3 / DNA repair protein Ku70 / DNA repair protein Ku80 / Histone H4
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 Å
AuthorsLu W / He Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2026
Title: DNA-PK driven nucleosome unwrapping enables NHEJ in chromatin
Authors: Lu W / Vogt A / Lees-Miller SP / He Y
History
DepositionDec 10, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74422.png

Downloads & links

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Map

FileDownload / File: emd_74422.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomplex of a Ku bound N7 nucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.1423465 - 0.3969426
Average (Standard dev.)0.0029392007 (±0.017506195)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74422_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_74422_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local reconstruction of Ku

Fileemd_74422_additional_1.map
AnnotationLocal reconstruction of Ku
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: low resolution consensus map

Fileemd_74422_additional_2.map
Annotationlow resolution consensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local reconstruction of N7

Fileemd_74422_additional_3.map
AnnotationLocal reconstruction of N7
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Ku bound to Nucleosome with 7bp overhang

EntireName: Complex of Ku bound to Nucleosome with 7bp overhang
Components
  • Complex: Complex of Ku bound to Nucleosome with 7bp overhang
    • Complex: Nucleosome with 7bp overhang
      • DNA: DNA (154-mer)
      • DNA: DNA (154-mer)
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: Ku70/80
      • Protein or peptide: X-ray repair cross-complementing protein 6
      • Protein or peptide: X-ray repair cross-complementing protein 5
  • Ligand: water

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Supramolecule #1: Complex of Ku bound to Nucleosome with 7bp overhang

SupramoleculeName: Complex of Ku bound to Nucleosome with 7bp overhang / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 152.5 KDa

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Supramolecule #2: Nucleosome with 7bp overhang

SupramoleculeName: Nucleosome with 7bp overhang / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: Ku70/80

SupramoleculeName: Ku70/80 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA (154-mer)

MacromoleculeName: DNA (154-mer) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.768418 KDa
SequenceString: (DG)(DA)(DT)(DC)(DG)(DC)(DT)(DA)(DT)(DC) (DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC) (DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG) (DA) (DC)(DT)(DA)(DG)(DG)(DG) ...String:
(DG)(DA)(DT)(DC)(DG)(DC)(DT)(DA)(DT)(DC) (DG)(DG)(DA)(DT)(DG)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DC)(DT)(DG)(DA)(DC)(DA)(DC) (DG)(DT)(DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG) (DA) (DC)(DT)(DA)(DG)(DG)(DG)(DA)(DG) (DT)(DA)(DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT) (DG)(DG) (DC)(DG)(DG)(DT)(DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG) (DA)(DC)(DA) (DG)(DC)(DG)(DC)(DG)(DT) (DA)(DC)(DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT) (DA)(DA)(DG)(DC) (DG)(DG)(DT)(DG)(DC) (DT)(DA)(DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC) (DT)(DA)(DC)(DG)(DA) (DC)(DC)(DA)(DA) (DT)(DT)(DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC) (DT)(DC)(DG)(DG)(DC)(DA) (DC)(DC)(DG) (DG)(DG)(DA)(DT)(DT)(DC)(DT)(DC)(DG)(DA) (DT)

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Macromolecule #2: DNA (154-mer)

MacromoleculeName: DNA (154-mer) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.306152 KDa
SequenceString: (DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String:
(DA)(DT)(DC)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DG)(DA)(DT)(DA)(DG)(DC)(DG)(DA)(DT) (DC)

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Macromolecule #3: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.859927 KDa
Recombinant expressionOrganism: Escherichia coli HB101 (bacteria)
SequenceString:
VKKPHRYRPG TVALREIRRY QKSTELLIRK LPFQRLVREI AQDFKTDLRF QSSAVMALQE ASEAYLVALF EDTNLCAIHA KRVTIMPKD IQLARRIRGE RA

UniProtKB: Histone H3

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Macromolecule #4: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 9.99077 KDa
Recombinant expressionOrganism: Escherichia coli HB101 (bacteria)
SequenceString:
KRHRKVLRDN IQGITKPAIR RLARRGGVKR ISGLIYEETR GVLKVFLENV IRDAVTYTEH AKRKTVTAMD VVYALKRQGR TLYGFGG

UniProtKB: Histone H4

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Macromolecule #5: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 24.946154 KDa
Recombinant expressionOrganism: Escherichia coli HB101 (bacteria)
SequenceString: GKQGGKTRAK AKTRSSRAGL QFPVGRVHRL LRKGNYAERV GAGAPVYLAA VLEYLTAEIL ELAGNAARDN KKTRIIPRHL QLAVRNDEE LNKLLGRVTI AQGGVLPNIQ SVLLPKKQGG KTRAKAKTRS SRAGLQFPVG RVHRLLRKGN YAERVGAGAP V YLAAVLEY ...String:
GKQGGKTRAK AKTRSSRAGL QFPVGRVHRL LRKGNYAERV GAGAPVYLAA VLEYLTAEIL ELAGNAARDN KKTRIIPRHL QLAVRNDEE LNKLLGRVTI AQGGVLPNIQ SVLLPKKQGG KTRAKAKTRS SRAGLQFPVG RVHRLLRKGN YAERVGAGAP V YLAAVLEY LTAEILELAG NAARDNKKTR IIPRHLQLAV RNDEELNKLL GRVTIAQGGV LPNIQSVLLP K

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Macromolecule #6: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.179959 KDa
Recombinant expressionOrganism: Escherichia coli HB101 (bacteria)
SequenceString:
KKRRKTRKES YAIYVYKVLK QVHPDTGISS KAMSIMNSFV NDVFERIAGE ASRLAHYNKR STITSREIQT AVRLLLPGEL AKHAVSEGT KAVTKYTSAK

UniProtKB: Histone H2B

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Macromolecule #7: X-ray repair cross-complementing protein 6

MacromoleculeName: X-ray repair cross-complementing protein 6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.998793 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: KYSGRDSLIF LVDASKAMFE SQSEDELTPF DMSIQCIQSV YISKIISSDR DLLAVVFYGT EKDKNSVNFK NIYVLQELDN PGAKRILEL DQFKGQQGQK RFQDMMGHGS DYSLSEVLWV CANLFSDVQF KMSHKRIMLF TNEDNPHGND SAKASRARTK A GDLRDTGI ...String:
KYSGRDSLIF LVDASKAMFE SQSEDELTPF DMSIQCIQSV YISKIISSDR DLLAVVFYGT EKDKNSVNFK NIYVLQELDN PGAKRILEL DQFKGQQGQK RFQDMMGHGS DYSLSEVLWV CANLFSDVQF KMSHKRIMLF TNEDNPHGND SAKASRARTK A GDLRDTGI FLDLMHLKKP GGFDISLFYR DIISIAEDED LRVHFEESSK LEDLLRKVRA KETRKRALSR LKLKLNKDIV IS VGIYNLV QKALKPPPIK LYRETNEPVK TKTRTFNTST GGLLLPSDTK RSQIYGSRQI ILEKEETEEL KRFDDPGLML MGF KPLVLL KKHHYLRPSL FVYPEESLVI GSSTLFSALL IKCLEKEVAA LCRYTPRRNI PPYFVALVPQ EEELDDQKIQ VTPP GFQLV FLPFADDKRK MPFTEKIMAT PEQVGKMKAI VEKLRFTYRS DSFENPVLQQ HFRNLEALAL DLMEPEQAVD LTLPK VEAM NKRLGSLVDE FKELVYPPDY

UniProtKB: DNA repair protein Ku70

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Macromolecule #8: X-ray repair cross-complementing protein 5

MacromoleculeName: X-ray repair cross-complementing protein 5 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.972969 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: NKAAVVLCMD VGFTMSNSIP GIESPFEQAK KVITMFVQRQ VFAENKDEIA LVLFGTDGTD NPLSGGDQYQ NITVHRHLML PDFDLLEDI ESKIQPGSQQ ADFLDALIVS MDVIQHETIG KKFEKRHIEI FTDLSSRFSK SQLDIIIHSL KKCDISLQFF L PFSLGKED ...String:
NKAAVVLCMD VGFTMSNSIP GIESPFEQAK KVITMFVQRQ VFAENKDEIA LVLFGTDGTD NPLSGGDQYQ NITVHRHLML PDFDLLEDI ESKIQPGSQQ ADFLDALIVS MDVIQHETIG KKFEKRHIEI FTDLSSRFSK SQLDIIIHSL KKCDISLQFF L PFSLGKED GSGDRGDGPF RLGGHGPSFP LKGITEQQKE GLEIVKMVMI SLEGEDGLDE IYSFSESLRK LCVFKKIERH SI HWPCRLT IGSNLSIRIA AYKSILQERV KKTWTVVDAK TLKKEDIQKE TVYCLNDDDE TEVLKEDIIQ GFRYGSDIVP FSK VDEEQM KYKSEGKCFS VLGFCKSSQV QRRFFMGNQV LKVFAARDDE AAAVALSSLI HALDDLDMVA IVRYAYDKRA NPQV GVAFP HIKHNYECLV YVQLPFMEDL RQYMFSSLKN SKKYAPTEAQ LNAVDALIDS MSLAKKDEKT DTLEDLFPTT KIPNP RFQR LFQCLLHRAL HPREPLPPIQ QHIWNMLNPP AEVTTKSQIP LSKIKTLFPL IE

UniProtKB: DNA repair protein Ku80

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 1 / 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 stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 4.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
In silico model: Initial model was generated de novo using cryoSPARC ab initio reconstruction from the curated particle set.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 81691
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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