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9iax

DNA-PK, LX4, XLF - Catalytic domain of L4

Method: ELECTRON MICROSCOPY Dmax: 277.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-dependent protein kinase catalytic subunit

OrganismNot specified

UniProt P78527

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–DNA Heteromer Protein × 8 DNA 2 PDB declaration: decameric（10） Consistent with all polymer counts Chain A； UniProt 1–4128 Not recorded X-ray repair cross-complementing protein 6 × 1 （P12956） X-ray repair cross-complementing protein 5 × 1 （P13010） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） DNA repair protein XRCC4 × 2 （Q13426） DNA ligase 4 × 1 （P49917） DNA × 1 DNA × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.97 Å

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 9IAX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5LUQ Crystal Structure of Human DNA-dependent Protein Kinase Catalytic Subunit (DNA-PKcs) Deposited 2016-09-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–2575（2574 aa）
Chain A 2774–4127（1354 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 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 0.437
5LUQ Crystal Structure of Human DNA-dependent Protein Kinase Catalytic Subunit (DNA-PKcs) Deposited 2016-09-09 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 2–2575（2574 aa）
Chain B 2774–4127（1354 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 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 0.437
5W1R Cryo-EM structure of DNAPKcs Deposited 2017-06-04 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4128（4128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
5Y3R Cryo-EM structure of Human DNA-PK Holoenzyme Deposited 2017-07-29 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain C 10–4128（4119 aa） Fragment：UNP residues 10-4128
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
6ZFP Cryo-EM structure of DNA-PKcs (State 2) Deposited 2020-06-17 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4128（4128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.24 Å
6ZH2 Cryo-EM structure of DNA-PKcs (State 1) Deposited 2020-06-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4128（4128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.92 Å
6ZH4 Cryo-EM structure of DNA-PKcs (State 3) Deposited 2020-06-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4128（4128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
6ZH6 Cryo-EM structure of DNA-PKcs:Ku80ct194 Deposited 2020-06-21 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–4128（4128 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
6ZH8 Cryo-EM structure of DNA-PKcs:DNA Deposited 2020-06-21 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 1–4128（4128 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
6ZHA Cryo-EM structure of DNA-PK monomer Deposited 2020-06-21 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–4128（4128 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 6 PDB declaration: decameric
Chain A 1–4128（4128 aa）
Chain F 1–4128（4128 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
7K0Y Cryo-EM structure of activated-form DNA-PK (complex VI) Deposited 2020-09-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain A 1–4128（4128 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
7K10 CryoEM structure of activated-form FATKIN domain of DNA-PK Deposited 2020-09-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4128（4128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7K11 CryoEM structure of inactivated-form FATKIN domain of DNA-PK Deposited 2020-09-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4128（4128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.21 Å
7K19 CryoEM structure of DNA-PK catalytic subunit complexed with DNA (Complex I) Deposited 2020-09-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 1–4128（4128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7K1B CryoEM structure of DNA-PK catalytic subunit complexed with DNA (Complex II) Deposited 2020-09-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 1–4128（4128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
7K1J CryoEM structure of inactivated-form DNA-PK (Complex III) Deposited 2020-09-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain A 1–4128（4128 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain A 1–4128（4128 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain A 1–4128（4128 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
7LT3 NHEJ Long-range synaptic complex Deposited 2021-02-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain C 1–4128（4128 aa）
Chain L 1–4128（4128 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain A 1–4128（4128 aa）
Chain F 1–4128（4128 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 experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain A 1–4128（4128 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
7OTM Cryo-EM structure of DNA-PKcs in complex with NU7441 Deposited 2021-06-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4128（4128 aa）
Not recorded 2R4 8-(dibenzo[b,d]thiophen-4-yl)-2-(morpholin-4-yl)-4H-chromen-4-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.33 Å
7OTP DNA-PKcs in complex with ATPgammaS-Mg Deposited 2021-06-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4128（4128 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7OTV DNA-PKcs in complex with wortmannin Deposited 2021-06-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4128（4128 aa）
Not recorded KWT (1S,6BR,9AS,11R,11BR)-9A,11B-DIMETHYL-1-[(METHYLOXY)METHYL]-3,6,9-TRIOXO-1,6,6B,7,8,9,9A,10,11,11B-DECAHYDRO-3H-FURO[4, 3,2-DE]INDENO[4,5-H][2]BENZOPYRAN-11-YL ACETATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.24 Å
7OTW DNA-PKcs in complex with AZD7648 Deposited 2021-06-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4128（4128 aa）
Not recorded MBW 7-methyl-2-[(7-methyl-[1,2,4]triazolo[1,5-a]pyridin-6-yl)amino]-9-(oxan-4-yl)purin-8-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.99 Å
7OTY DNA-PKcs in complex with M3814 Deposited 2021-06-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–4128（4128 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 2.96 Å
7SGL DNA-PK complex of DNA end processing Deposited 2021-10-06 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–4128（4128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: heptameric
Chain A 1–4128（4128 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–4128（4128 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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
7TYR Cryo-EM structure of the basal state of the Artemis:DNA-PKcs complex (see COMPND 13/14) Deposited 2022-02-14 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–4128（4128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Plunge-freeze was performed using a home-made manual plunger at typical indoor humidity (Los Angeles, CA) and at room temperature.
Resolution 3.33 Å
7Z87 DNA-PK in the active state Deposited 2022-03-16 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 1–4128（4128 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–4128（4128 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
8BH3 DNA-PK Ku80 mediated dimer bound to PAXX Deposited 2022-10-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain A 1–4128（4128 aa）
Chain S 1–4128（4128 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain A 1–4128（4128 aa）
Chain F 1–4128（4128 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain A 1–4128（4128 aa）
Chain S 1–4128（4128 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 25-meric
Chain A 1–4128（4128 aa）
Chain F 1–4128（4128 aa）
Chain S 1–4128（4128 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
8EZ9 Dimeric complex of DNA-PKcs Deposited 2022-10-31 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–4128（4128 aa）
Chain L 1–4128（4128 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.67 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain C 1–4128（4128 aa）
Chain L 1–4128（4128 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain C 1–4128（4128 aa）
Chain L 1–4128（4128 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–4128（4128 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
9G9L DNA-PK + Polymerase lambda Deposited 2024-07-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain A 1–4128（4128 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 experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain S 1–4128（4128 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
9Q9F DNA-PK bound to a 153 bp H2AX nucleosome model 1 Deposited 2025-02-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain O 1–4128（4128 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: 13-meric
Chain O 1–4128（4128 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 22 PDB declaration: 26-meric
Chain O 1–4128（4128 aa）
Chain o 1–4128（4128 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 30-meric
Chain O 1–4128（4128 aa）
Chain o 1–4128（4128 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

46 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PRKDC_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–4128； UniProt 1–4128

X-ray repair cross-complementing protein 6

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–DNA Heteromer Protein × 8 DNA 2 PDB declaration: decameric（10） Consistent with all polymer counts Chain B； UniProt 1–609 Not recorded DNA-dependent protein kinase catalytic subunit × 1 （P78527） X-ray repair cross-complementing protein 5 × 1 （P13010） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） DNA repair protein XRCC4 × 2 （Q13426） DNA ligase 4 × 1 （P49917） DNA × 1 DNA × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.97 Å

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 9IAX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1JEQ Crystal Structure of the Ku Heterodimer Deposited 2001-06-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
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 8.5；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 Different construct Different oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–609（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 oligomeric state Different ligand/ion 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 oligomeric state 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 oligomeric state 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 method 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 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 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 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 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 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 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 oligomeric state 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 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 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 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 oligomeric state 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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–609（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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–609（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 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
9IGW Ku70/80 bound to 147 bp nucleosome Deposited 2025-02-20 Different oligomeric state 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 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 oligomeric state Different ligand/ion 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 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 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 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 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 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 oligomeric state 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 oligomeric state 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 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 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 XRCC6_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–609； UniProt 1–609

X-ray repair cross-complementing protein 5

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–DNA Heteromer Protein × 8 DNA 2 PDB declaration: decameric（10） Consistent with all polymer counts Chain C； UniProt 1–732 Not recorded DNA-dependent protein kinase catalytic subunit × 1 （P78527） X-ray repair cross-complementing protein 6 × 1 （P12956） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） DNA repair protein XRCC4 × 2 （Q13426） DNA ligase 4 × 1 （P49917） DNA × 1 DNA × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.97 Å

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 9IAX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1JEQ Crystal Structure of the Ku Heterodimer Deposited 2001-06-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
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 Different construct Different oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state 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 oligomeric state 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 method 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 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 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 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 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 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 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 oligomeric state 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 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 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 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 oligomeric state 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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
9IGW Ku70/80 bound to 147 bp nucleosome Deposited 2025-02-20 Different oligomeric state 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 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain A 1–732（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 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 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 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 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 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 oligomeric state 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 oligomeric state 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 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 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 XRCC5_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–732； UniProt 1–732

Non-homologous end-joining factor 1

Homo sapiens

UniProt Q9H9Q4

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–DNA Heteromer Protein × 8 DNA 2 PDB declaration: decameric（10） Consistent with all polymer counts Chain D； UniProt 1–299 Chain M； UniProt 1–299 Not recorded DNA-dependent protein kinase catalytic subunit × 1 （P78527） X-ray repair cross-complementing protein 6 × 1 （P12956） X-ray repair cross-complementing protein 5 × 1 （P13010） DNA repair protein XRCC4 × 2 （Q13426） DNA ligase 4 × 1 （P49917） DNA × 1 DNA × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.97 Å

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 9IAX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2QM4 Crystal structure of human XLF/Cernunnos, a non-homologous end-joining factor Deposited 2007-07-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–233（233 aa）
Chain B 1–233（233 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；23% PEG 6000, 0.1M Bis-Tris-Propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Resolution 2.30 Å R-free 0.239
2QM4 Crystal structure of human XLF/Cernunnos, a non-homologous end-joining factor Deposited 2007-07-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–233（233 aa）
Chain D 1–233（233 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；23% PEG 6000, 0.1M Bis-Tris-Propane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Resolution 2.30 Å R-free 0.239
2R9A Crystal structure of human XLF Deposited 2007-09-12 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–224（224 aa） Fragment：N-terminal fragment, unp residues 1-224
Chain B 1–224（224 aa） Fragment：N-terminal fragment, unp residues 1-224
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；273 K；pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K
Resolution 2.50 Å R-free 0.287
3Q4F Crystal structure of xrcc4/xlf-cernunnos complex Deposited 2010-12-23 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 1–224（224 aa） Fragment：unp residues 1-224
Chain B 1–224（224 aa） Fragment：unp residues 1-224
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；9% v/v MPD, 50 mM MgSO4, 0.1 M Na Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 5.50 Å R-free 0.309
3Q4F Crystal structure of xrcc4/xlf-cernunnos complex Deposited 2010-12-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 1–224（224 aa） Fragment：unp residues 1-224
Chain F 1–224（224 aa） Fragment：unp residues 1-224
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；9% v/v MPD, 50 mM MgSO4, 0.1 M Na Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 5.50 Å R-free 0.309
3RWR Crystal structure of the human XRCC4-XLF complex Deposited 2011-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–224（224 aa） Fragment：unp residues 1-224
Chain E 1–224（224 aa） Fragment：unp residues 1-224
Chain H 1–224（224 aa） Fragment：unp residues 1-224
Chain I 1–224（224 aa） Fragment：unp residues 1-224
Not recorded TBR HEXATANTALUM DODECABROMIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.8M Ammonium citrate, pH 8.0, 20 mM Barium chloride dihydrate, 400 mM sodium thiocyanate, 0.5 mM tantalum bromide, 60% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.94 Å R-free 0.326
3SR2 Crystal Structure of Human XLF-XRCC4 Complex Deposited 2011-07-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–224（224 aa） Fragment：UNP Residues 1-224
Chain D 1–224（224 aa） Fragment：UNP Residues 1-224
Chain G 1–224（224 aa） Fragment：UNP Residues 1-224
Chain H 1–224（224 aa） Fragment：UNP Residues 1-224
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；303.15 K；protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, 100 mM HEPES, pH7.8 under argon., vapor diffusion, temperature 303.15K
Resolution 3.97 Å R-free 0.369
3SR2 Crystal Structure of Human XLF-XRCC4 Complex Deposited 2011-07-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–224（224 aa） Fragment：UNP Residues 1-224
Chain D 1–224（224 aa） Fragment：UNP Residues 1-224
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；303.15 K；protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, 100 mM HEPES, pH7.8 under argon., vapor diffusion, temperature 303.15K
Resolution 3.97 Å R-free 0.369
3SR2 Crystal Structure of Human XLF-XRCC4 Complex Deposited 2011-07-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 1–224（224 aa） Fragment：UNP Residues 1-224
Chain H 1–224（224 aa） Fragment：UNP Residues 1-224
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；303.15 K；protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, 100 mM HEPES, pH7.8 under argon., vapor diffusion, temperature 303.15K
Resolution 3.97 Å R-free 0.369
3W03 XLF-XRCC4 complex Deposited 2012-10-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–233（233 aa） Fragment：UNP residues 1-233
Chain B 1–233（233 aa） Fragment：UNP residues 1-233
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M Tris pH7.5, 2M Sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 8.49 Å R-free 0.360
6ERG Complex of XLF and heterodimer Ku bound to DNA Deposited 2017-10-18 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 × 3 PDB declaration: pentameric
Chain F 287–299（13 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain C 287–299（13 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 mutation/modification 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 M 281–299（19 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain T 281–299（19 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
7LSY NHEJ Short-range synaptic complex Deposited 2021-02-18 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: heptadecameric
Chain H 1–299（299 aa）
Chain I 1–299（299 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain H 1–299（299 aa）
Chain I 1–299（299 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain Q 1–299（299 aa）
Chain R 1–299（299 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 experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain F 1–299（299 aa）
Chain G 1–299（299 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
7ZYG CryoEM structure of Ku heterodimer bound to DNA, PAXX and XLF Deposited 2022-05-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain F 1–299（299 aa）
Not recorded PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.68 Å
8BHV DNA-PK XLF mediated dimer bound to PAXX Deposited 2022-11-01 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain Q 1–299（299 aa）
Chain R 1–299（299 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 oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain f 1–299（299 aa）
Chain m 1–299（299 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 25-meric
Chain Q 1–299（299 aa）
Chain R 1–299（299 aa）
Chain X 1–299（299 aa）
Chain Y 1–299（299 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain H 1–299（299 aa）
Chain I 1–299（299 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain H 1–299（299 aa）
Chain I 1–299（299 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
9CQ3 The gap-filling complex with Pol mu engaged in the NHEJ pathway Deposited 2024-07-19 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain C 1–299（299 aa）
Chain c 1–299（299 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain C 1–299（299 aa）
Chain c 1–299（299 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain C 1–299（299 aa）
Chain c 1–299（299 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
9IOL Cryo-EM structure of the complex of DNA, Ku70/80, and laXLF. Deposited 2024-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain M 287–299（13 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain C 1–299（299 aa）
Chain c 1–299（299 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain C 1–299（299 aa）
Chain c 1–299（299 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain C 1–299（299 aa）
Chain c 1–299（299 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

25 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NHEJ1_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–299； UniProt 1–299 Author chain M； PDBConstruct 1–299； UniProt 1–299

DNA repair protein XRCC4

Homo sapiens

UniProt Q13426

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–DNA Heteromer Protein × 8 DNA 2 PDB declaration: decameric（10） Consistent with all polymer counts Chain G； UniProt 1–336 Chain H； UniProt 1–336 Not recorded DNA-dependent protein kinase catalytic subunit × 1 （P78527） X-ray repair cross-complementing protein 6 × 1 （P12956） X-ray repair cross-complementing protein 5 × 1 （P13010） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） DNA ligase 4 × 1 （P49917） DNA × 1 DNA × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.97 Å

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 9IAX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1FU1 CRYSTAL STRUCTURE OF HUMAN XRCC4 Deposited 2000-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–203（203 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-203
Chain B 1–203（203 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-203
Mutation：T135I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：T135I Non-standard monomer：Yes (specific site not provided by mmCIF) ACY ACETIC ACID × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Ammonium sulphate, magnesium acetate, DTT, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.263
1FU1 CRYSTAL STRUCTURE OF HUMAN XRCC4 Deposited 2000-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–203（203 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-203
Chain B 1–203（203 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-203
Mutation：T135I Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：T135I Non-standard monomer：Yes (specific site not provided by mmCIF) ACY ACETIC ACID × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Ammonium sulphate, magnesium acetate, DTT, cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.70 Å R-free 0.263
1IK9 CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX Deposited 2001-05-03 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–213（213 aa） Fragment：XRCC4 FRAGMENT, RESIDUES 1-213
Chain B 1–213（213 aa） Fragment：XRCC4 FRAGMENT, RESIDUES 1-213
Mutation：C93A,C128A,C130A,C165A Mutation：C93A,C128A,C130A,C165A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG6000, MES, xylitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.30 Å R-free 0.266
3II6 Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV. Deposited 2009-07-31 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–203（203 aa） Fragment：residues 1-203
Chain B 1–203（203 aa） Fragment：residues 1-203
Mutation：A60E, I134T Mutation：A60E, I134T No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；100mM Sodium/Potassium phosphate, 15% PEG 8000 MME, 200mM Sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.280
3II6 Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV. Deposited 2009-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–203（203 aa） Fragment：residues 1-203
Chain D 1–203（203 aa） Fragment：residues 1-203
Mutation：A60E, I134T Mutation：A60E, I134T CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；100mM Sodium/Potassium phosphate, 15% PEG 8000 MME, 200mM Sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.280
3MUD Structure of the Tropomyosin Overlap Complex from Chicken Smooth Muscle Deposited 2010-05-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 2–137（136 aa）
Chain B 2–137（136 aa）
Mutation：I134T, L249N,I134T Mutation：I134T, L249N,I134T EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；18% MePEG 2000, 100 mM Bis-Tris, 120 mM MgSO4 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.20 Å R-free 0.250
3Q4F Crystal structure of xrcc4/xlf-cernunnos complex Deposited 2010-12-23 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 G 1–157（157 aa） Fragment：unp residues 1-157
Chain H 1–157（157 aa） Fragment：unp residues 1-157
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；9% v/v MPD, 50 mM MgSO4, 0.1 M Na Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 5.50 Å R-free 0.309
3Q4F Crystal structure of xrcc4/xlf-cernunnos complex Deposited 2010-12-23 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–157（157 aa） Fragment：unp residues 1-157
Chain D 1–157（157 aa） Fragment：unp residues 1-157
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；9% v/v MPD, 50 mM MgSO4, 0.1 M Na Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 5.50 Å R-free 0.309
3RWR Crystal structure of the human XRCC4-XLF complex Deposited 2011-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–157（157 aa） Fragment：unp residues 1-157
Chain B 1–157（157 aa） Fragment：unp residues 1-157
Chain F 1–157（157 aa） Fragment：unp residues 1-157
Chain G 1–157（157 aa） Fragment：unp residues 1-157
Not recorded TBR HEXATANTALUM DODECABROMIDE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.8M Ammonium citrate, pH 8.0, 20 mM Barium chloride dihydrate, 400 mM sodium thiocyanate, 0.5 mM tantalum bromide, 60% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.94 Å R-free 0.326
3SR2 Crystal Structure of Human XLF-XRCC4 Complex Deposited 2011-07-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–140（140 aa）
Chain B 1–140（140 aa）
Chain E 1–140（140 aa）
Chain F 1–140（140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；303.15 K；protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, 100 mM HEPES, pH7.8 under argon., vapor diffusion, temperature 303.15K
Resolution 3.97 Å R-free 0.369
3SR2 Crystal Structure of Human XLF-XRCC4 Complex Deposited 2011-07-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–140（140 aa）
Chain B 1–140（140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；303.15 K；protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, 100 mM HEPES, pH7.8 under argon., vapor diffusion, temperature 303.15K
Resolution 3.97 Å R-free 0.369
3SR2 Crystal Structure of Human XLF-XRCC4 Complex Deposited 2011-07-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–140（140 aa）
Chain F 1–140（140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；303.15 K；protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, 100 mM HEPES, pH7.8 under argon., vapor diffusion, temperature 303.15K
Resolution 3.97 Å R-free 0.369
3W03 XLF-XRCC4 complex Deposited 2012-10-17 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–164（164 aa） Fragment：UNP residues 1-164
Chain D 1–164（164 aa） Fragment：UNP residues 1-164
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M Tris pH7.5, 2M Sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 8.49 Å R-free 0.360
4XA4 Crystal Structure of the coiled-coil surrounding Skip 3 of MYH7 Deposited 2014-12-12 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–147（146 aa） Fragment：UNP Q13426 residues 2-147,UNP P12883 residues 1551-1609
Chain B 2–147（146 aa） Fragment：UNP Q13426 residues 2-147,UNP P12883 residues 1551-1609
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% (w/v) polyethylene glycol 1500, 250 mM tetramethylammonium chloride, 100 mM 3-[4-(2-Hydroxyethyl)-1-piperazinyl]propanesulfonic acid (HEPPS)
Resolution 2.33 Å R-free 0.274
5CHX Crystal Structure of amino acids 1590-1657 of MYH7 Deposited 2015-07-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–143（142 aa） Fragment：UNP Q13426 residues 2-143, UNP P12833 1590-1657
Chain B 2–143（142 aa） Fragment：UNP Q13426 residues 2-143, UNP P12833 1590-1657
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；16% (w/v) MEPEG 2000, 250 mM potassium nitrate, 100 mM 3-(N-morpholino)propanesulfonic acid (MOPS)
Resolution 2.30 Å R-free 0.265
5CHX Crystal Structure of amino acids 1590-1657 of MYH7 Deposited 2015-07-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–143（142 aa） Fragment：UNP Q13426 residues 2-143, UNP P12833 1590-1657
Chain B 2–143（142 aa） Fragment：UNP Q13426 residues 2-143, UNP P12833 1590-1657
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；16% (w/v) MEPEG 2000, 250 mM potassium nitrate, 100 mM 3-(N-morpholino)propanesulfonic acid (MOPS)
Resolution 2.30 Å R-free 0.265
5CJ0 Crystal Structure of Amino Acids 1631-1692 of MYH7 Deposited 2015-07-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–142（141 aa） Fragment：UNP Q13426 residues 2-142, UNP P12883 residues 1631-1692
Chain B 2–142（141 aa） Fragment：UNP Q13426 residues 2-142, UNP P12883 residues 1631-1692
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；14% (w/v) MEPEG 5000, 200 mM glycine, 100 mM bistrispropane pH 7.0.
Resolution 2.30 Å R-free 0.238
5CJ4 Crystal Structure of Amino Acids 1562-1622 of MYH7 Deposited 2015-07-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–144（143 aa） Fragment：UNP Q13426 residues 2-144, UNP P12883 1562-1622
Chain B 2–144（143 aa） Fragment：UNP Q13426 residues 2-144, UNP P12883 1562-1622
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；23% (w/v) PEG 4000, 500 mM NaCl, 100 mM triethanolamine pH 8.0.
Resolution 3.10 Å R-free 0.280
5CJ4 Crystal Structure of Amino Acids 1562-1622 of MYH7 Deposited 2015-07-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 2–144（143 aa） Fragment：UNP Q13426 residues 2-144, UNP P12883 1562-1622
Chain D 2–144（143 aa） Fragment：UNP Q13426 residues 2-144, UNP P12883 1562-1622
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；23% (w/v) PEG 4000, 500 mM NaCl, 100 mM triethanolamine pH 8.0.
Resolution 3.10 Å R-free 0.280
5WJ7 Crystal Structure of Amino Acids 1733-1797 of Human Beta Cardiac Myosin Fused to Xrcc4 Deposited 2017-07-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–132（131 aa） Fragment：UNP Q13426 residues 2-132, UNP P12883 residues 1733-1797
Chain B 2–132（131 aa） Fragment：UNP Q13426 residues 2-132, UNP P12883 residues 1733-1797
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；16% (w/v) Methyl-Ether PEG 5K, 300 mM glycine, 100 mM triethanolamine pH 7.5
Resolution 2.50 Å R-free 0.249
5WLZ Crystal Structure of Amino Acids 1677-1758 of Human Beta Cardiac Myosin Fused to Xrcc4 Deposited 2017-07-28 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–132（131 aa） Fragment：UNP Q13426 residues 2-132, UNP P12883 residues 1677-1758
Chain B 2–132（131 aa） Fragment：UNP Q13426 residues 2-132, UNP P12883 residues 1677-1758
Chain C 2–132（131 aa） Fragment：UNP Q13426 residues 2-132, UNP P12883 residues 1677-1758
Chain D 2–132（131 aa） Fragment：UNP Q13426 residues 2-132, UNP P12883 residues 1677-1758
Mutation：E29K, E51K, D57A, D58T, E62N, C93R, E98K,C128D, C132A Mutation：E29K, E51K, D57A, D58T, E62N, C93R, E98K,C128D, C132A Mutation：E29K, E51K, D57A, D58T, E62N, C93R, E98K,C128D, C132A Mutation：E29K, E51K, D57A, D58T, E62N, C93R, E98K,C128D, C132A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；8-10% methyl-ether polyethylene glycol (MEPEG) 5K, 300 mM glycine, bis-tris propane pH 7.0, 1.5-3.0% (w/v) jeffamine M-600
Resolution 3.50 Å R-free 0.249
6ABO human XRCC4 and IFFO1 complex Deposited 2018-07-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–213（213 aa） Fragment：UNP residues 1-213
Not recorded GOL GLYCEROL × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.1M Sodium cacodylate pH6.0, 50mM Calcium acetate, 20-25% MPD, 1M Ammonium sulfate
Resolution 2.65 Å R-free 0.273
7LSY NHEJ Short-range synaptic complex Deposited 2021-02-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: heptadecameric
Chain F 1–336（336 aa）
Chain G 1–336（336 aa）
Chain O 1–336（336 aa）
Chain P 1–336（336 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain F 1–336（336 aa）
Chain G 1–336（336 aa）
Chain O 1–336（336 aa）
Chain P 1–336（336 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
7M3P Xrcc4-Spc110p(164-207) fusion Deposited 2021-03-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–132（131 aa）
Chain B 2–132（131 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；13% PEG3350 and 0.2 M magnesium formate
Resolution 2.00 Å R-free 0.247
7NFC Cryo-EM structure of NHEJ super-complex (dimer) Deposited 2021-02-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain K 1–336（336 aa）
Chain L 1–336（336 aa）
Chain N 1–336（336 aa）
Chain O 1–336（336 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 experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain H 1–336（336 aa）
Chain I 1–336（336 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
8BH3 DNA-PK Ku80 mediated dimer bound to PAXX Deposited 2022-10-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain G 1–336（336 aa）
Chain H 1–336（336 aa）
Chain P 1–336（336 aa）
Chain Q 1–336（336 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain K 1–336（336 aa）
Chain L 1–336（336 aa）
Chain N 1–336（336 aa）
Chain O 1–336（336 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain G 1–336（336 aa）
Chain H 1–336（336 aa）
Chain P 1–336（336 aa）
Chain Q 1–336（336 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 25-meric
Chain K 1–336（336 aa）
Chain L 1–336（336 aa）
Chain N 1–336（336 aa）
Chain O 1–336（336 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain F 1–336（336 aa）
Chain G 1–336（336 aa）
Chain O 1–336（336 aa）
Chain P 1–336（336 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain F 1–336（336 aa）
Chain G 1–336（336 aa）
Chain O 1–336（336 aa）
Chain P 1–336（336 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
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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain D 1–336（336 aa）
Chain E 1–336（336 aa）
Chain d 1–336（336 aa）
Chain e 1–336（336 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain D 1–336（336 aa）
Chain E 1–336（336 aa）
Chain d 1–336（336 aa）
Chain e 1–336（336 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain D 1–336（336 aa）
Chain E 1–336（336 aa）
Chain d 1–336（336 aa）
Chain e 1–336（336 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
9GD7 DNA-PK Ku80 mediated dimer bound to DNA polymerase Lambda and DNA ligase 4/XRCC4 Deposited 2024-08-05 Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain P 1–336（336 aa）
Chain Q 1–336（336 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
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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain D 1–336（336 aa）
Chain E 1–336（336 aa）
Chain d 1–336（336 aa）
Chain e 1–336（336 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain D 1–336（336 aa）
Chain E 1–336（336 aa）
Chain d 1–336（336 aa）
Chain e 1–336（336 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain D 1–336（336 aa）
Chain E 1–336（336 aa）
Chain d 1–336（336 aa）
Chain e 1–336（336 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

33 other PDB entries and 40 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name XRCC4_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain G； PDBConstruct 1–336； UniProt 1–336 Author chain H； PDBConstruct 1–336； UniProt 1–336

DNA ligase 4

Homo sapiens

UniProt P49917

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–DNA Heteromer Protein × 8 DNA 2 PDB declaration: decameric（10） Consistent with all polymer counts Chain K； UniProt 1–911 Not recorded DNA-dependent protein kinase catalytic subunit × 1 （P78527） X-ray repair cross-complementing protein 6 × 1 （P12956） X-ray repair cross-complementing protein 5 × 1 （P13010） Non-homologous end-joining factor 1 × 2 （Q9H9Q4） DNA repair protein XRCC4 × 2 （Q13426） DNA × 1 DNA × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.97 Å

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 9IAX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IK9 CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX Deposited 2001-05-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 748–784（37 aa） Fragment：LINKER CONNECTING BRCT DOMAINS, RESIDUES 748-784
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG6000, MES, xylitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.30 Å R-free 0.266
2E2W Solution structure of the first BRCT domain of human DNA ligase IV Deposited 2006-11-17 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 654–759（106 aa） Fragment：BRCT domain
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；293 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.23mM uniformly 13C and 15N labelled protein; 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3, 10% D2O, 90% H2O | 10% D2O, 90% H2O
Resolution not provided
3II6 Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV. Deposited 2009-07-31 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain X 654–911（258 aa） Fragment：C-Terminal tandem BRCT domains, residues 654-911
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；100mM Sodium/Potassium phosphate, 15% PEG 8000 MME, 200mM Sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.280
3II6 Structure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV. Deposited 2009-07-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Y 654–911（258 aa） Fragment：C-Terminal tandem BRCT domains, residues 654-911
Not recorded CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；100mM Sodium/Potassium phosphate, 15% PEG 8000 MME, 200mM Sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.280
3VNN Crystal Structure of a sub-domain of the nucleotidyltransferase (adenylation) domain of human DNA ligase IV Deposited 2012-01-17 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 268–406（139 aa） Fragment：A sub-domain of the nucleotidyltransferase (adenylation) domain, UNP residues 268-405
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；7.5% PEG 6000, 100mM MES, 0.01mg/ml papain, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.90 Å R-free 0.305
3W1B Crystal Structure of Human DNA ligase IV-Artemis Complex (Mercury Derivative) Deposited 2012-11-14 Different construct Different oligomeric state 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） Fragment：Catalytic region, UNP residues 1-609
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 SO4 SULFATE ION × 10 HG MERCURY (II) ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；2M ammonium sulfate, 10mM YCl, 100mM MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.40 Å R-free 0.225
3W1G Crystal Structure of Human DNA ligase IV-Artemis Complex (Native) Deposited 2012-11-15 Different construct Different oligomeric state 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） Fragment：Catalytic region, UNP residues 1-609
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SO4 SULFATE ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；2M ammonium sulfate, 10mM YCl, 100mM MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.55 Å R-free 0.234
3W5O Crystal Structure of Human DNA ligase IV Deposited 2013-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–609（609 aa） Fragment：catalytic region, UNP residues 1-609
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SO4 SULFATE ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；291 K；2M ammonium sulfate, 10mM YCl, 100mM MES, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.84 Å R-free 0.245
3W5O Crystal Structure of Human DNA ligase IV Deposited 2013-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–609（609 aa） Fragment：catalytic region, UNP residues 1-609
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 SO4 SULFATE ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；291 K；2M ammonium sulfate, 10mM YCl, 100mM MES, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.84 Å R-free 0.245
4HTO Crystal structure of the DBD domain of human DNA ligase IV Apo form Deposited 2012-11-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–240（240 aa） Fragment：DNA binding domain
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；16 % PEG 3350, 200 mM (NH4)3PO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；16 % PEG 3350, 200 mM (NH4)3SO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.81 Å R-free 0.259
4HTP Crystal structure of the DBD domain of human DNA ligase IV bound to Artemis peptide Deposited 2012-11-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–240（240 aa） Fragment：DNA binding domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；18% PEG 1000, 200 mM Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.25 Å R-free 0.249
4HTP Crystal structure of the DBD domain of human DNA ligase IV bound to Artemis peptide Deposited 2012-11-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–240（240 aa） Fragment：DNA binding domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.15 K；18% PEG 1000, 200 mM Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Resolution 2.25 Å R-free 0.249
6BKF Lysyl-adenylate form of human LigIV catalytic domain with bound DNA substrate in open conformation Deposited 2017-11-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 1–620（620 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；76.5mM HEPES pH 7.5, 15.3% PEG 4K, 7.65% isopropanol, 13.5% glycerol, 10mM MgCl2
Resolution 3.25 Å R-free 0.316
6BKG Human LigIV catalytic domain with bound DNA-adenylate intermediate in closed conformation Deposited 2017-11-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 1–620（620 aa）
Not recorded CL CHLORIDE ION × 2 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 AMP ADENOSINE MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；78.2mM HEPES pH 7.5, 15.64% PEG4000, 7.82% isopropanol, 13.8% glycerol
Resolution 2.40 Å R-free 0.245
7D9K DNA binding domain of human DNA Ligase IV - Wild type Deposited 2020-10-13 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 1–240（240 aa） Fragment：DNA binding domain
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277.15 K；0.1 M Tris pH 8.0, 20 % SOKALAN CP 42, 5% Methanol
Resolution 2.90 Å R-free 0.299
7D9Y DNA binding domain of human DNA Ligase IV mutant - A3V Deposited 2020-10-14 Different construct Different mutation/modification 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 1–240（240 aa）
Mutation：A3V No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277.15 K；0.125 M Tris pH 8.0, 20 % SOKALAN CP 42, 7.5% Methanol
Resolution 2.76 Å R-free 0.276
7LSY NHEJ Short-range synaptic complex Deposited 2021-02-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: heptadecameric
Chain X 1–911（911 aa）
Chain Y 1–911（911 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain X 1–911（911 aa）
Chain Y 1–911（911 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain M 1–911（911 aa）
Chain P 1–911（911 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 experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain J 1–911（911 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
8BH3 DNA-PK Ku80 mediated dimer bound to PAXX Deposited 2022-10-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain I 1–911（911 aa）
Chain R 1–911（911 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain M 1–911（911 aa）
Chain P 1–911（911 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain I 1–911（911 aa）
Chain R 1–911（911 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 25-meric
Chain M 1–911（911 aa）
Chain P 1–911（911 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 22-meric
Chain X 1–911（911 aa）
Chain Y 1–911（911 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain X 1–911（911 aa）
Chain Y 1–911（911 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
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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain F 1–911（911 aa）
Chain f 1–911（911 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain F 1–911（911 aa）
Chain f 1–911（911 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain F 1–911（911 aa）
Chain f 1–911（911 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
9GD7 DNA-PK Ku80 mediated dimer bound to DNA polymerase Lambda and DNA ligase 4/XRCC4 Deposited 2024-08-05 Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain E 1–911（911 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
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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 16 PDB declaration: eicosameric
Chain F 1–911（911 aa）
Chain f 1–911（911 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain F 1–911（911 aa）
Chain f 1–911（911 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 conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 14 PDB declaration: octadecameric
Chain F 1–911（911 aa）
Chain f 1–911（911 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

30 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DNLI4_HUMAN
Isoform —
PDB entities 6
Chains and sequence ranges Author chain K； PDBConstruct 1–911； UniProt 1–911

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 9iax

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9iax
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9iax
Deposition date deposition_date2025-02-11
Structure title titleDNA-PK, LX4, XLF - Catalytic domain of L4
Keywords keywordsKinase, NHEJ, cryo-EM, DNA-PK, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier74.12 Å
Radius of gyration Rg (electron density) rg_electron74.38 Å
Forward intensity I(0) i07244250000.00
Molecular weight molecular_weight729790.0 kDa
Excluded volume excluded_volume916910 ų
Envelope volume envelope_volume1553900 ų
Hydration-shell volume shell_volume175180 ų
Envelope diameter envelope_diameter269.3 Å
Shell Rg shell_rg72.27 Å
Envelope Rg envelope_rg74.40 Å
Shape Rg shape_rg74.43 Å
Total Rg total_rg74.17 Å
Total atoms total_atoms51268
Residues n_residues6382
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 dmax277.1 Å
Rg (real space) rg_real78.52 Å
Rg uncertainty (real space) rg_real_error1.71 Å
I(0) (real space) i0_real7.3080e+09
I(0) uncertainty (real space) i0_real_error1.6030e+08
Rg (reciprocal space) rg_reciprocal73.68 Å
I(0) (reciprocal space) i0_reciprocal7236000000.0000
Solution quality estimate total_estimate0.8619
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary92.4 Å
Skewness Skewness skewness0.628
Kurtosis Kurtosis kurtosis0.163
Angular range angular_range— – 0.1050 Å−1
Current regularization parameter α current_alpha0.9431
Highest regularization parameter α highest_alpha547400000.0000
Real-space data points n_real_points22
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.706; Stabil: 0.847; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.590
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (1)

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9. Files and Curves (10)