Current Protein Identity：P13010
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1JEQ Crystal Structure of the Ku Heterodimer Deposited 2001-06-18 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
0–564（565 aa）
|
Not recorded | No recorded non-water small molecule | 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 |
| 1JEY Crystal Structure of the Ku heterodimer bound to DNA Deposited 2001-06-19 | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 3 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 4 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric（10） Consistent with all polymers |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric（7） Consistent with all polymers |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric（7） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric（7） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric（7） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: heptadecameric（17） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric（18） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric（7） Consistent with all polymers |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: octadecameric（18） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric（18） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 25-meric（25） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric（22） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric（6） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric（18） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric（18） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric（7） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric（12） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric（20） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric（18） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric（18） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: 14-meric（14） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric（13） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric（13） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 26-meric（26） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 30-meric（30） Consistent with all polymers |
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 |