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- EMDB-52550: Ku70/80, DNA bound to Polymerase Mu -

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Basic information

Entry
Database: EMDB / ID: EMD-52550
TitleKu70/80, DNA bound to Polymerase Mu
Map data
Sample
  • Complex: Ku70/80 heterodimer with BRCT domain of Polymerase mu
    • Protein or peptide: X-ray repair cross-complementing protein 6
    • Protein or peptide: X-ray repair cross-complementing protein 5
    • Protein or peptide: DNA-directed DNA/RNA polymerase mu
    • DNA: DNA (5'-D(P*GP*GP*TP*GP*CP*AP*GP*CP*AP*CP*AP*GP*TP*G)-3')
    • DNA: DNA (5'-D(P*GP*CP*AP*CP*TP*GP*TP*GP*CP*TP*GP*CP*AP*C)-3')
KeywordsPolymerase / enzyme / cryo-EM / NHEJ / DNA BINDING PROTEIN
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 / regulation of smooth muscle cell proliferation / cellular response to X-ray ...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 / regulation of smooth muscle cell proliferation / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / nuclear telomere cap complex / Cytosolic sensors of pathogen-associated DNA / IRF3-mediated induction of type I IFN / recombinational repair / regulation of telomere maintenance / protein localization to chromosome, telomeric region / U3 snoRNA binding / positive regulation of neurogenesis / cellular hyperosmotic salinity response / 2-LTR circle formation / hematopoietic stem cell proliferation / telomeric repeat DNA binding / DNA 3'-5' helicase / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / ATP-dependent activity, acting on DNA / telomere maintenance via telomerase / somatic hypermutation of immunoglobulin genes / site of DNA damage / activation of innate immune response / neurogenesis / telomere maintenance / B cell differentiation / cyclin binding / DNA helicase activity / DNA-(apurinic or apyrimidinic site) lyase / cellular response to leukemia inhibitory factor / Nonhomologous End-Joining (NHEJ) / small-subunit processome / cellular response to gamma radiation / protein-DNA complex / double-strand break repair via nonhomologous end joining / enzyme activator activity / double-strand break repair / double-stranded DNA binding / scaffold protein binding / secretory granule lumen / DNA recombination / transcription regulator complex / DNA-directed DNA polymerase / ficolin-1-rich granule lumen / damaged DNA binding / DNA-directed DNA polymerase activity / chromosome, telomeric region / transcription cis-regulatory region binding / ribonucleoprotein complex / innate immune response / negative regulation of DNA-templated transcription / DNA damage response / Neutrophil degranulation / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / plasma membrane / 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 / DNA-directed DNA/RNA polymerase mu / 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 / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase beta-like, N-terminal domain / DNA polymerase lambda lyase domain superfamily / Helix-hairpin-helix domain / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / von Willebrand factor (vWF) type A domain / BRCT domain profile. / von Willebrand factor, type A / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
DNA repair protein Ku70 / DNA repair protein Ku80 / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.05 Å
AuthorsChaplin AK / Amin H
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: Structural and functional insights into the interaction between Ku70/80 and Pol X family polymerases in NHEJ.
Authors: Philippe Frit / Himani Amin / Sayma Zahid / Nadia Barboule / Chloe Hall / Gurdip Matharu / Steven W Hardwick / Jeanne Chauvat / Sébastien Britton / Dima Y Chirgadze / Virginie Ropars / Jean- ...Authors: Philippe Frit / Himani Amin / Sayma Zahid / Nadia Barboule / Chloe Hall / Gurdip Matharu / Steven W Hardwick / Jeanne Chauvat / Sébastien Britton / Dima Y Chirgadze / Virginie Ropars / Jean-Baptiste Charbonnier / Patrick Calsou / Amanda K Chaplin /
Abstract: Non-homologous end joining (NHEJ) is the main repair pathway for double-strand DNA breaks (DSBs) in mammals. DNA polymerases lambda (Pol λ) and mu (Pol μ), members of the Pol X family, play a key ...Non-homologous end joining (NHEJ) is the main repair pathway for double-strand DNA breaks (DSBs) in mammals. DNA polymerases lambda (Pol λ) and mu (Pol μ), members of the Pol X family, play a key role in this process. However, their interaction within the NHEJ complexes is unclear. Here, we present cryo-EM structures of Pol λ in complex with the DNA-PK long-range synaptic complex, and Pol μ bound to Ku70/80-DNA. These structures identify interaction sites between Ku70/80 and Pol X BRCT domains. Using mutants at the proteins interface in functional assays including cell transfection with an original gap-filling reporter, we define the role of the BRCT domain in the recruitment and activity of the two Pol X members in NHEJ and in their contribution to cell survival following DSBs. Finally, we propose a unified model for the interaction of all Pol X members with Ku70/80.
History
DepositionJan 14, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52550.png

Downloads & links

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Map

FileDownload / File: emd_52550.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.73 Å/pix.
x 168 pix.
= 290.048 Å		1.73 Å/pix.
x 168 pix.
= 290.048 Å		1.73 Å/pix.
x 168 pix.
= 290.048 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.23
Minimum - Maximum-0.37216365 - 0.73769814
Average (Standard dev.)0.0022537205 (±0.027156493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions168168168
Spacing168168168
CellA=B=C: 290.048 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52550_half_map_1.map
Projections & Slices
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Density Histograms

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Half map: #1

Fileemd_52550_half_map_2.map
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Sample components

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Entire : Ku70/80 heterodimer with BRCT domain of Polymerase mu

EntireName: Ku70/80 heterodimer with BRCT domain of Polymerase mu
Components
  • Complex: Ku70/80 heterodimer with BRCT domain of Polymerase mu
    • Protein or peptide: X-ray repair cross-complementing protein 6
    • Protein or peptide: X-ray repair cross-complementing protein 5
    • Protein or peptide: DNA-directed DNA/RNA polymerase mu
    • DNA: DNA (5'-D(P*GP*GP*TP*GP*CP*AP*GP*CP*AP*CP*AP*GP*TP*G)-3')
    • DNA: DNA (5'-D(P*GP*CP*AP*CP*TP*GP*TP*GP*CP*TP*GP*CP*AP*C)-3')

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Supramolecule #1: Ku70/80 heterodimer with BRCT domain of Polymerase mu

SupramoleculeName: Ku70/80 heterodimer with BRCT domain of Polymerase mu / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: X-ray repair cross-complementing protein 6

MacromoleculeName: X-ray repair cross-complementing protein 6 / type: protein_or_peptide / ID: 1 / 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: 56.654352 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SLIFLVDASK AMFESQSEDE LTPFDMSIQC IQSVYISKII SSDRDLLAVV FYGTEKDKNS VNFKNIYVLQ ELDNPGAKRI LELDQFKGQ QGQKRFQDMM GHGSDYSLSE VLWVCANLFS DVQFKMSHKR IMLFTNEDNP HGNDSAKASR ARTKAGDLRD T GIFLDLMH ...String:
SLIFLVDASK AMFESQSEDE LTPFDMSIQC IQSVYISKII SSDRDLLAVV FYGTEKDKNS VNFKNIYVLQ ELDNPGAKRI LELDQFKGQ QGQKRFQDMM GHGSDYSLSE VLWVCANLFS DVQFKMSHKR IMLFTNEDNP HGNDSAKASR ARTKAGDLRD T GIFLDLMH LKKPGGFDIS LFYRDIISIA EDEDLRVHFE ESSKLEDLLR KVRAKETRKR ALSRLKLKLN KDIVISVGIY NL VQKALKP PPIKLYRETN EPVKTKTRTF NTSTGGLLLP SDTKRSQIYG SRQIILEKEE TEELKRFDDP GLMLMGFKPL VLL KKHHYL RPSLFVYPEE SLVIGSSTLF SALLIKCLEK EVAALCRYTP RRNIPPYFVA LVPQEEELDD QKIQVTPPGF QLVF LPFAD DKRKMPFTEK IMATPEQVGK MKAIVEKLRF TYRSDSFENP VLQQHFRNLE ALALDLMEPE QAVDLTLPKV EAMNK RLGS LVDEFKELV

UniProtKB: DNA repair protein Ku70

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Macromolecule #2: X-ray repair cross-complementing protein 5

MacromoleculeName: X-ray repair cross-complementing protein 5 / type: protein_or_peptide / ID: 2 / 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: 60.430305 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GNKAAVVLCM DVGFTMSNSI PGIESPFEQA KKVITMFVQR QVFAENKDEI ALVLFGTDGT DNPLSGGDQY QNITVHRHLM LPDFDLLED IESKIQPGSQ QADFLDALIV SMDVIQHETI GKKFEKRHIE IFTDLSSRFS KSQLDIIIHS LKKCDISLQF F LPFSLGKE ...String:
GNKAAVVLCM DVGFTMSNSI PGIESPFEQA KKVITMFVQR QVFAENKDEI ALVLFGTDGT DNPLSGGDQY QNITVHRHLM LPDFDLLED IESKIQPGSQ QADFLDALIV SMDVIQHETI GKKFEKRHIE IFTDLSSRFS KSQLDIIIHS LKKCDISLQF F LPFSLGKE DGSGDRGDGP FRLGGHGPSF PLKGITEQQK EGLEIVKMVM ISLEGEDGLD EIYSFSESLR KLCVFKKIER HS IHWPCRL TIGSNLSIRI AAYKSILQER VKKTWTVVDA KTLKKEDIQK ETVYCLNDDD ETEVLKEDII QGFRYGSDIV PFS KVDEEQ MKYKSEGKCF SVLGFCKSSQ VQRRFFMGNQ VLKVFAARDD EAAAVALSSL IHALDDLDMV AIVRYAYDKR ANPQ VGVAF PHIKHNYECL VYVQLPFMED LRQYMFSSLK NSKKYAPTEA QLNAVDALID SMSLAKKDEK TDTLEDLFPT TKIPN PRFQ RLFQCLLHRA LHPREPLPPI QQHIWNMLNP PAEVTTKSQI PLSKIKTL

UniProtKB: DNA repair protein Ku80

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Macromolecule #3: DNA-directed DNA/RNA polymerase mu

MacromoleculeName: DNA-directed DNA/RNA polymerase mu / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.192678 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AIYLVEPRMG RSRRAFLTGL ARSKGFRVLD ACSSEATHVV MEETSAEEAV SWQERRMAAA PPGCTPPALL DISWLTESLG AGQPVPVEC RHRL

UniProtKB: DNA-directed DNA/RNA polymerase mu

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Macromolecule #4: DNA (5'-D(P*GP*GP*TP*GP*CP*AP*GP*CP*AP*CP*AP*GP*TP*G)-3')

MacromoleculeName: DNA (5'-D(P*GP*GP*TP*GP*CP*AP*GP*CP*AP*CP*AP*GP*TP*G)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.345829 KDa
SequenceString:
(DG)(DG)(DT)(DG)(DC)(DA)(DG)(DC)(DA)(DC) (DA)(DG)(DT)(DG)

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Macromolecule #5: DNA (5'-D(P*GP*CP*AP*CP*TP*GP*TP*GP*CP*TP*GP*CP*AP*C)-3')

MacromoleculeName: DNA (5'-D(P*GP*CP*AP*CP*TP*GP*TP*GP*CP*TP*GP*CP*AP*C)-3')
type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.256766 KDa
SequenceString:
(DG)(DC)(DA)(DC)(DT)(DG)(DT)(DG)(DC)(DT) (DG)(DC)(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

Concentration1.6 mg/mL
BufferpH: 7.6
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
200.0 mMNaClSodium Chloride
0.5 mMC10H16N2O8EDTA
0.2 mMMgCl2Magnesium Chloride
5.0 mMC4H10O2S2DTT
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average exposure time: 2.0 sec. / Average electron dose: 1.007399378 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: 2.0 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: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23808
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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