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1jeq

Crystal Structure of the Ku Heterodimer

Method: X-RAY DIFFRACTION Dmax: 121.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

KU70

Homo sapiens

UniProt P12956

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 0–608 Not recorded KU80 × 1 （P13010） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；14% PEG 4000, 900 mM sarcosine, 140 mM magnesium chloride, 100 mM Tris-HCl (pH 8.5), VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.70 Å R-free 0.283

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1JEQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1JEY Crystal Structure of the Ku heterodimer bound to DNA Deposited 2001-06-19 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 0–608（609 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；26% polyethylene glycol 350 monomethyl ether, 50 mM Tris-HCL pH 8.0, 5 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.50 Å R-free 0.280
3RZX Mouse importin alpha-Ku70 NLS peptide complex Deposited 2011-05-12 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 537–558（22 aa） Fragment：Nuclear localization signal
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Sodium Citrate, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.61 Å R-free 0.223
5Y3R Cryo-EM structure of Human DNA-PK Holoenzyme Deposited 2017-07-29 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 34–534（501 aa） Fragment：UNP residues 34-534
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
6ERF Complex of APLF factor and Ku heterodimer bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–544（544 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bris Tris propane 13% PEG 3350 150 mM Na nirate
Resolution 3.01 Å R-free 0.227
6ERF Complex of APLF factor and Ku heterodimer bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain C 1–544（544 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bris Tris propane 13% PEG 3350 150 mM Na nirate
Resolution 3.01 Å R-free 0.227
6ERF Complex of APLF factor and Ku heterodimer bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain E 1–544（544 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bris Tris propane 13% PEG 3350 150 mM Na nirate
Resolution 3.01 Å R-free 0.227
6ERF Complex of APLF factor and Ku heterodimer bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain G 1–544（544 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bris Tris propane 13% PEG 3350 150 mM Na nirate
Resolution 3.01 Å R-free 0.227
6ERG Complex of XLF and heterodimer Ku bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–544（544 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；18% PEG 3350, 150 mM Na sulfate , 100 mM Bis-Tris-Propane
Resolution 2.90 Å R-free 0.244
6ERG Complex of XLF and heterodimer Ku bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain D 1–544（544 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；18% PEG 3350, 150 mM Na sulfate , 100 mM Bis-Tris-Propane
Resolution 2.90 Å R-free 0.244
6ERH Complex of XLF and heterodimer Ku bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–544（544 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；18% PEG 3350, 150 mM sodium sulfate, and 100 mM Bis-Tris-Propane
Resolution 2.80 Å R-free 0.252
6ERH Complex of XLF and heterodimer Ku bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain C 1–544（544 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；18% PEG 3350, 150 mM sodium sulfate, and 100 mM Bis-Tris-Propane
Resolution 2.80 Å R-free 0.252
6ZHA Cryo-EM structure of DNA-PK monomer Deposited 2020-06-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.91 Å
6ZHE Cryo-EM structure of DNA-PK dimer Deposited 2020-06-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric
Chain B 1–609（609 aa）
Chain G 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.24 Å
7AXZ Ku70/80 complex apo form Deposited 2020-11-10 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7K0Y Cryo-EM structure of activated-form DNA-PK (complex VI) Deposited 2020-09-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain B 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7K1J CryoEM structure of inactivated-form DNA-PK (Complex III) Deposited 2020-09-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain B 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7K1K CryoEM structure of inactivated-form DNA-PK (Complex IV) Deposited 2020-09-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain B 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7K1N CryoEM structure of inactivated-form DNA-PK (Complex V) Deposited 2020-09-08 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain B 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7LSY NHEJ Short-range synaptic complex Deposited 2021-02-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: heptadecameric
Chain A 1–600（600 aa）
Chain J 1–600（600 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.40 Å
7LT3 NHEJ Long-range synaptic complex Deposited 2021-02-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain A 1–609（609 aa）
Chain J 1–609（609 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7NFC Cryo-EM structure of NHEJ super-complex (dimer) Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain B 1–609（609 aa）
Chain G 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.14 Å
7NFE Cryo-EM structure of NHEJ super-complex (monomer) Deposited 2021-02-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.29 Å
7SGL DNA-PK complex of DNA end processing Deposited 2021-10-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–609（609 aa）
Not recorded MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7SU3 CryoEM structure of DNA-PK complex VII Deposited 2021-11-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain B 1–609（609 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7Z6O X-Ray studies of Ku70/80 reveal the binding site for IP6 Deposited 2022-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 1–609（609 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；24% PEG3350, 200mM Na2SO4, 100mM BTP, 5 mM b-mercaptoethanol
Resolution 3.70 Å R-free 0.271
7Z87 DNA-PK in the active state Deposited 2022-03-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–609（609 aa）
Not recorded 1IX (~{S})-[2-chloranyl-4-fluoranyl-5-(7-morpholin-4-ylquinazolin-4-yl)phenyl]-(6-methoxypyridazin-3-yl)methanol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
7Z88 DNA-PK in the intermediate state Deposited 2022-03-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–609（609 aa）
Not recorded 1IX (~{S})-[2-chloranyl-4-fluoranyl-5-(7-morpholin-4-ylquinazolin-4-yl)phenyl]-(6-methoxypyridazin-3-yl)methanol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
7ZT6 Cryo-EM structure of Ku 70/80 bound to inositol hexakisphosphate Deposited 2022-05-09 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–609（609 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7ZVT CryoEM structure of Ku heterodimer bound to DNA Deposited 2022-05-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 1–609（609 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.74 Å
7ZWA CryoEM structure of Ku heterodimer bound to DNA and PAXX Deposited 2022-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–609（609 aa）
Not recorded PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7ZYG CryoEM structure of Ku heterodimer bound to DNA, PAXX and XLF Deposited 2022-05-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–609（609 aa）
Not recorded PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.68 Å
8AG4 Vaccinia C16 protein bound to Ku70/Ku80 Deposited 2022-07-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.46 Å
8AG5 Vaccinia C16 protein bound to Ku70/Ku80 Deposited 2022-07-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.47 Å
8ASC Ku70/80 binds to the Ku-binding motif of PAXX Deposited 2022-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: octadecameric
Chain A 1–544（544 aa）
Chain E 1–544（544 aa）
Chain K 1–544（544 aa）
Chain O 1–544（544 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；12% PEG- 3350; 0.1 M Bis-Tris Propane pH 8.5; 0.3 M Ammonium Sulfate
Resolution 2.95 Å R-free 0.298
8BH3 DNA-PK Ku80 mediated dimer bound to PAXX Deposited 2022-10-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain B 1–609（609 aa）
Chain T 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.55 Å
8BHV DNA-PK XLF mediated dimer bound to PAXX Deposited 2022-11-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain a 1–609（609 aa）
Chain h 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.51 Å
8BHY DNA-PK Ku80 mediated dimer bound to PAXX and XLF Deposited 2022-11-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain B 1–609（609 aa）
Chain T 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.33 Å
8BOT Cryo-EM structure of NHEJ supercomplex(trimer) Deposited 2022-11-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 25-meric
Chain B 1–609（609 aa）
Chain G 1–609（609 aa）
Chain T 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.76 Å
8EZA NHEJ Long-range complex with PAXX Deposited 2022-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain A 1–609（609 aa）
Chain J 1–609（609 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.39 Å
8EZB NHEJ Long-range complex with ATP Deposited 2022-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain A 1–609（609 aa）
Chain J 1–609（609 aa）
Not recorded MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.90 Å
8RD4 Telomeric RAP1:DNA-PK complex Deposited 2023-12-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain E 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.58 Å
9CQ3 The gap-filling complex with Pol mu engaged in the NHEJ pathway Deposited 2024-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain A 1–609（609 aa）
Chain a 1–609（609 aa）
Not recorded MG MAGNESIUM ION × 2 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9CQ6 The ligation complex in the NHEJ pathway Deposited 2024-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain A 1–609（609 aa）
Chain a 1–609（609 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9CQC The ligation complex like in the NHEJ pathway Deposited 2024-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain A 1–609（609 aa）
Chain a 1–609（609 aa）
Not recorded DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9G9L DNA-PK + Polymerase lambda Deposited 2024-07-25 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain B 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.63 Å
9GD7 DNA-PK Ku80 mediated dimer bound to DNA polymerase Lambda and DNA ligase 4/XRCC4 Deposited 2024-08-05 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain T 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
9GYF Ku70/80 with PAXX peptide mutation K193R Deposited 2024-10-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–609（609 aa）
Not recorded PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9HZG Ku70/80 bound to WRN-exo Deposited 2025-01-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–609（609 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
9I04 Ku70/80, DNA bound to Polymerase Mu Deposited 2025-01-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 37–529（493 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
9IAX DNA-PK, LX4, XLF - Catalytic domain of L4 Deposited 2025-02-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
9IGW Ku70/80 bound to 147 bp nucleosome Deposited 2025-02-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain K 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
9IGX Ku70/80 bound to 153 bp nucleosome Deposited 2025-02-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain K 34–534（501 aa）
Chain M 34–534（501 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å
9IOL Cryo-EM structure of the complex of DNA, Ku70/80, and laXLF. Deposited 2024-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–609（609 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 2OP (2S)-2-HYDROXYPROPANOIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9N81 A gap-filling complex with Pol mu engaged in the NHEJ Pathway Deposited 2025-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain A 1–609（609 aa）
Chain a 1–609（609 aa）
Not recorded MG MAGNESIUM ION × 1 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9N82 The ligation (AMP-Lys) complex in the NHEJ pathway Deposited 2025-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain A 1–609（609 aa）
Chain a 1–609（609 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9N83 The ligation complex in the NHEJ pathway Deposited 2025-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain A 1–609（609 aa）
Chain a 1–609（609 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9Q80 Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome Deposited 2025-02-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain K 1–609（609 aa）
Chain M 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9Q8X Ku70/80 bound to a 153 bp H2AX nucleosome Deposited 2025-02-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain K 1–609（609 aa）
Chain M 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
9Q9F DNA-PK bound to a 153 bp H2AX nucleosome model 1 Deposited 2025-02-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain K 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.54 Å
9QCR DNA-PK bound to 153 bp H2AX nucleosome model 2 Deposited 2025-03-05 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain K 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.37 Å
9QCS Ku80 mediated DNA-PK dimer bound to 153 bp H2AX nucleosome Deposited 2025-03-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 26-meric
Chain K 1–609（609 aa）
Chain M 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
9QMS DNA-PK bound to 153 bp H2AX nucleosome with ATPyS Deposited 2025-03-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 30-meric
Chain K 1–609（609 aa）
Chain M 1–609（609 aa）
Chain k 1–609（609 aa）
Chain m 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å

57 other PDB entries and 62 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KU70_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–609； UniProt 0–608

KU80

Homo sapiens

UniProt P13010

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 0–564 Not recorded KU70 × 1 （P12956） X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；14% PEG 4000, 900 mM sarcosine, 140 mM magnesium chloride, 100 mM Tris-HCl (pH 8.5), VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.70 Å R-free 0.283

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 1JEQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1JEY Crystal Structure of the Ku heterodimer bound to DNA Deposited 2001-06-19 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 0–564（565 aa） Fragment：residues 1-565
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；26% polyethylene glycol 350 monomethyl ether, 50 mM Tris-HCL pH 8.0, 5 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.50 Å R-free 0.280
1Q2Z The 3D solution structure of the C-terminal region of Ku86 Deposited 2003-07-28 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 591–708（118 aa） Fragment：Ku86CTR (591-709)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure ambient
NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure ambient
NMR sample composition 1mM U-15N; 20mM Phosphate; 100mM NaCl; 1mM NaN3 | 90% H2O/10% D2O
NMR sample composition 1mM U-13C,15N; 20mM Phosphate; 100mM NaCl; 1mM NaN3 | 90% H2O/10% D2O
NMR sample composition 1mM U-15N; 20mM Phosphate; 100mM NaCl; 1mM NaN3; 5% n-octyl-penta(ethylene glycol):octanol 0.96:1 | 90% H2O/10% D2O
Resolution not provided
1RW2 Three-dimensional structure of Ku80 CTD Deposited 2003-12-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 565–709（145 aa） Fragment：Ku80 C-terminal Domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 100 mM phosphate buffer；Pressure 1
NMR sample composition Approximately 1 mM N-15/C-13 labeled protein in 100 mM phosphate buffer, pH 6.0, and 5 mM DTT | 100% D2O
NMR sample composition Approximately 1 mM N-15/C-13 labeled protein in 100 mM phosphate buffer, pH 6.0, and 5 mM DTT | 90% H2O/10% D2O
NMR sample composition Approximately 1 mM N-15 labeled protein in 100 mM phosphate buffer, pH 6.0, an | 90% H2O/10% D2O
Resolution not provided
3RZ9 Mouse importin alpha-Ku80 NLS peptide complex Deposited 2011-05-11 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 559–571（13 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Sodium Citrate, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.29 Å R-free 0.218
5Y3R Cryo-EM structure of Human DNA-PK Holoenzyme Deposited 2017-07-29 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 6–541（536 aa） Fragment：UNP residues 6-541
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.60 Å
6ERF Complex of APLF factor and Ku heterodimer bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 2–555（554 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bris Tris propane 13% PEG 3350 150 mM Na nirate
Resolution 3.01 Å R-free 0.227
6ERF Complex of APLF factor and Ku heterodimer bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain D 2–555（554 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bris Tris propane 13% PEG 3350 150 mM Na nirate
Resolution 3.01 Å R-free 0.227
6ERF Complex of APLF factor and Ku heterodimer bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain F 2–555（554 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bris Tris propane 13% PEG 3350 150 mM Na nirate
Resolution 3.01 Å R-free 0.227
6ERF Complex of APLF factor and Ku heterodimer bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain H 2–555（554 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bris Tris propane 13% PEG 3350 150 mM Na nirate
Resolution 3.01 Å R-free 0.227
6ERG Complex of XLF and heterodimer Ku bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 2–555（554 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；18% PEG 3350, 150 mM Na sulfate , 100 mM Bis-Tris-Propane
Resolution 2.90 Å R-free 0.244
6ERG Complex of XLF and heterodimer Ku bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain E 2–555（554 aa）
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；18% PEG 3350, 150 mM Na sulfate , 100 mM Bis-Tris-Propane
Resolution 2.90 Å R-free 0.244
6ERH Complex of XLF and heterodimer Ku bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 2–555（554 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；18% PEG 3350, 150 mM sodium sulfate, and 100 mM Bis-Tris-Propane
Resolution 2.80 Å R-free 0.252
6ERH Complex of XLF and heterodimer Ku bound to DNA Deposited 2017-10-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain D 2–555（554 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；18% PEG 3350, 150 mM sodium sulfate, and 100 mM Bis-Tris-Propane
Resolution 2.80 Å R-free 0.252
6ZH6 Cryo-EM structure of DNA-PKcs:Ku80ct194 Deposited 2020-06-21 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 541–732（192 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
6ZHA Cryo-EM structure of DNA-PK monomer Deposited 2020-06-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain C 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.91 Å
6ZHE Cryo-EM structure of DNA-PK dimer Deposited 2020-06-23 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric
Chain C 1–732（732 aa）
Chain H 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.24 Å
7AXZ Ku70/80 complex apo form Deposited 2020-11-10 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7K0Y Cryo-EM structure of activated-form DNA-PK (complex VI) Deposited 2020-09-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain C 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7K17 Re-refined crystal structure of DNA-dependent protein kinase catalytic subunit complexed with Ku80 C-terminal helix Deposited 2020-09-07 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 541–732（192 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris, 200 mM NaCl, 30% glycerol, 10 mM EDTA, 18% PEG 8000
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris, 200 mM NaCl, 30% glycerol, 10 mM EDTA, 8% PEG 8000
Resolution 4.30 Å R-free 0.335
7K17 Re-refined crystal structure of DNA-dependent protein kinase catalytic subunit complexed with Ku80 C-terminal helix Deposited 2020-09-07 Different construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 541–732（192 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris, 200 mM NaCl, 30% glycerol, 10 mM EDTA, 18% PEG 8000
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Bis-Tris, 200 mM NaCl, 30% glycerol, 10 mM EDTA, 8% PEG 8000
Resolution 4.30 Å R-free 0.335
7K1J CryoEM structure of inactivated-form DNA-PK (Complex III) Deposited 2020-09-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain C 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7K1K CryoEM structure of inactivated-form DNA-PK (Complex IV) Deposited 2020-09-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain C 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7K1N CryoEM structure of inactivated-form DNA-PK (Complex V) Deposited 2020-09-08 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain C 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7LSY NHEJ Short-range synaptic complex Deposited 2021-02-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: heptadecameric
Chain B 1–732（732 aa）
Chain K 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.40 Å
7LT3 NHEJ Long-range synaptic complex Deposited 2021-02-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain B 1–732（732 aa）
Chain K 1–732（732 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
7NFC Cryo-EM structure of NHEJ super-complex (dimer) Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain C 1–732（732 aa）
Chain H 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.14 Å
7NFE Cryo-EM structure of NHEJ super-complex (monomer) Deposited 2021-02-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.29 Å
7SGL DNA-PK complex of DNA end processing Deposited 2021-10-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain C 1–732（732 aa）
Not recorded MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7SU3 CryoEM structure of DNA-PK complex VII Deposited 2021-11-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain C 1–732（732 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7SUD CryoEM structure of DNA-PK complex VIII Deposited 2021-11-16 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–732（732 aa）
Not recorded MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7Z6O X-Ray studies of Ku70/80 reveal the binding site for IP6 Deposited 2022-03-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 1–732（732 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；24% PEG3350, 200mM Na2SO4, 100mM BTP, 5 mM b-mercaptoethanol
Resolution 3.70 Å R-free 0.271
7Z87 DNA-PK in the active state Deposited 2022-03-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain C 1–732（732 aa）
Not recorded 1IX (~{S})-[2-chloranyl-4-fluoranyl-5-(7-morpholin-4-ylquinazolin-4-yl)phenyl]-(6-methoxypyridazin-3-yl)methanol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.91 Å
7Z88 DNA-PK in the intermediate state Deposited 2022-03-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain C 1–732（732 aa）
Not recorded 1IX (~{S})-[2-chloranyl-4-fluoranyl-5-(7-morpholin-4-ylquinazolin-4-yl)phenyl]-(6-methoxypyridazin-3-yl)methanol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
7ZT6 Cryo-EM structure of Ku 70/80 bound to inositol hexakisphosphate Deposited 2022-05-09 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–732（732 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7ZVT CryoEM structure of Ku heterodimer bound to DNA Deposited 2022-05-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain B 1–732（732 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.74 Å
7ZWA CryoEM structure of Ku heterodimer bound to DNA and PAXX Deposited 2022-05-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–732（732 aa）
Not recorded PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7ZYG CryoEM structure of Ku heterodimer bound to DNA, PAXX and XLF Deposited 2022-05-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain B 1–732（732 aa）
Not recorded PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.68 Å
8AG4 Vaccinia C16 protein bound to Ku70/Ku80 Deposited 2022-07-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.46 Å
8AG5 Vaccinia C16 protein bound to Ku70/Ku80 Deposited 2022-07-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.47 Å
8ASC Ku70/80 binds to the Ku-binding motif of PAXX Deposited 2022-08-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: octadecameric
Chain B 2–555（554 aa）
Chain F 2–555（554 aa）
Chain L 2–555（554 aa）
Chain P 2–555（554 aa）
Not recorded SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；290 K；12% PEG- 3350; 0.1 M Bis-Tris Propane pH 8.5; 0.3 M Ammonium Sulfate
Resolution 2.95 Å R-free 0.298
8BH3 DNA-PK Ku80 mediated dimer bound to PAXX Deposited 2022-10-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain C 1–732（732 aa）
Chain L 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.55 Å
8BHV DNA-PK XLF mediated dimer bound to PAXX Deposited 2022-11-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain b 1–732（732 aa）
Chain j 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.51 Å
8BHY DNA-PK Ku80 mediated dimer bound to PAXX and XLF Deposited 2022-11-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain C 1–732（732 aa）
Chain L 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.33 Å
8BOT Cryo-EM structure of NHEJ supercomplex(trimer) Deposited 2022-11-15 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 25-meric
Chain C 1–732（732 aa）
Chain H 1–732（732 aa）
Chain U 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.76 Å
8EZA NHEJ Long-range complex with PAXX Deposited 2022-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain B 1–732（732 aa）
Chain K 1–732（732 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.39 Å
8EZB NHEJ Long-range complex with ATP Deposited 2022-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain B 1–732（732 aa）
Chain K 1–732（732 aa）
Not recorded MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.90 Å
8RD4 Telomeric RAP1:DNA-PK complex Deposited 2023-12-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain F 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.58 Å
9CQ3 The gap-filling complex with Pol mu engaged in the NHEJ pathway Deposited 2024-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain B 1–732（732 aa）
Chain b 1–732（732 aa）
Not recorded MG MAGNESIUM ION × 2 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9CQ6 The ligation complex in the NHEJ pathway Deposited 2024-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain B 1–732（732 aa）
Chain b 1–732（732 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9CQC The ligation complex like in the NHEJ pathway Deposited 2024-07-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain B 1–732（732 aa）
Chain b 1–732（732 aa）
Not recorded DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9G9L DNA-PK + Polymerase lambda Deposited 2024-07-25 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain C 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.63 Å
9GD7 DNA-PK Ku80 mediated dimer bound to DNA polymerase Lambda and DNA ligase 4/XRCC4 Deposited 2024-08-05 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain L 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
9GYF Ku70/80 with PAXX peptide mutation K193R Deposited 2024-10-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–732（732 aa）
Not recorded PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9HZG Ku70/80 bound to WRN-exo Deposited 2025-01-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 1–732（732 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
9I04 Ku70/80, DNA bound to Polymerase Mu Deposited 2025-01-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain B 5–536（532 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.05 Å
9IAX DNA-PK, LX4, XLF - Catalytic domain of L4 Deposited 2025-02-11 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
9IGW Ku70/80 bound to 147 bp nucleosome Deposited 2025-02-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric
Chain L 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
9IGX Ku70/80 bound to 153 bp nucleosome Deposited 2025-02-20 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain L 6–545（540 aa）
Chain N 6–545（540 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å
9IOL Cryo-EM structure of the complex of DNA, Ku70/80, and laXLF. Deposited 2024-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–732（732 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 2OP (2S)-2-HYDROXYPROPANOIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.46 Å
9N81 A gap-filling complex with Pol mu engaged in the NHEJ Pathway Deposited 2025-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain B 1–732（732 aa）
Chain b 1–732（732 aa）
Not recorded MG MAGNESIUM ION × 1 DZ4 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9N82 The ligation (AMP-Lys) complex in the NHEJ pathway Deposited 2025-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain B 1–732（732 aa）
Chain b 1–732（732 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9N83 The ligation complex in the NHEJ pathway Deposited 2025-02-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain B 1–732（732 aa）
Chain b 1–732（732 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9Q80 Ku70/80 with Ku70 linker and SAP domain bound to a 153 bp H2AX nucleosome Deposited 2025-02-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain L 1–732（732 aa）
Chain N 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9Q8X Ku70/80 bound to a 153 bp H2AX nucleosome Deposited 2025-02-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric
Chain L 1–732（732 aa）
Chain N 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
9Q9F DNA-PK bound to a 153 bp H2AX nucleosome model 1 Deposited 2025-02-26 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain L 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.54 Å
9QCR DNA-PK bound to 153 bp H2AX nucleosome model 2 Deposited 2025-03-05 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain L 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.37 Å
9QCS Ku80 mediated DNA-PK dimer bound to 153 bp H2AX nucleosome Deposited 2025-03-05 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 26-meric
Chain L 1–732（732 aa）
Chain N 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.38 Å
9QMS DNA-PK bound to 153 bp H2AX nucleosome with ATPyS Deposited 2025-03-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 30-meric
Chain L 1–732（732 aa）
Chain N 1–732（732 aa）
Chain l 1–732（732 aa）
Chain n 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å

62 other PDB entries and 68 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KU86_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–565； UniProt 0–564

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 1jeq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1jeq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1jeq
Deposition date deposition_date2001-06-18
Structure title titleCrystal Structure of the Ku Heterodimer
Keywords keywords;double-strand DNA break repair, non-homologous end-joining, alpha/beta domain, beta barrel, helical C-terminal arm, sap domain, DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.24 Å
Radius of gyration Rg (electron density) rg_electron35.43 Å
Forward intensity I(0) i0217238000.00
Molecular weight molecular_weight122110.0 kDa
Excluded volume excluded_volume154550 ų
Envelope volume envelope_volume207340 ų
Hydration-shell volume shell_volume49522 ų
Envelope diameter envelope_diameter130.8 Å
Shell Rg shell_rg41.31 Å
Envelope Rg envelope_rg34.87 Å
Shape Rg shape_rg35.42 Å
Total Rg total_rg35.90 Å
Total atoms total_atoms8591
Residues n_residues1068
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax121.4 Å
Rg (real space) rg_real36.27 Å
Rg uncertainty (real space) rg_real_error0.80 Å
I(0) (real space) i0_real2.1720e+08
I(0) uncertainty (real space) i0_real_error3.1480e+06
Rg (reciprocal space) rg_reciprocal36.25 Å
I(0) (reciprocal space) i0_reciprocal217200000.0000
Solution quality estimate total_estimate0.8730
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.2 Å
Skewness Skewness skewness0.386
Kurtosis Kurtosis kurtosis-0.186
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha42220000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.823
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd1jeqa1
Class classa — All alpha proteins
Fold Fold folda.140 — LEM/SAP HeH motif
Superfamily Superfamily superfamilya.140.2 — SAP domain
Family Family familya.140.2.1 — SAP domain
Domain ID domain_idd1jeqa3
Class classb — All beta proteins
Fold Fold foldb.131 — SPOC domain-like
Superfamily Superfamily superfamilyb.131.1 — SPOC domain-like
Family Family familyb.131.1.1 — Ku70 subunit middle domain
Domain ID domain_idd1jeqa4
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.62 — vWA-like
Superfamily Superfamily superfamilyc.62.1 — vWA-like
Family Family familyc.62.1.3 — Ku70 subunit N-terminal domain
Domain ID domain_idd1jeqb1
Class classb — All beta proteins
Fold Fold foldb.131 — SPOC domain-like
Superfamily Superfamily superfamilyb.131.1 — SPOC domain-like
Family Family familyb.131.1.2 — Ku80 subunit middle domain
Domain ID domain_idd1jeqb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.62 — vWA-like
Superfamily Superfamily superfamilyc.62.1 — vWA-like
Family Family familyc.62.1.4 — Ku80 subunit N-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id1jeqA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily410 — von Willebrand factor, type A domain
Domain ID domain_id1jeqA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology290 — Ku70; Chain: A; Domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1jeqA03
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology970 — Ku70, bridge and pillars
Homologous superfamily homologous superfamily10 — Ku70, bridge and pillars
Domain ID domain_id1jeqA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1600 — Ku70; Chain: A; domain 4
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1jeqA05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology720 — Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1
Homologous superfamily homologous superfamily30 — SAP domain
Domain ID domain_id1jeqB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily410 — von Willebrand factor, type A domain
Domain ID domain_id1jeqB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology290 — Ku70; Chain: A; Domain 2
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1jeqB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1600 — Ku70; Chain: A; domain 4
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)