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9gd7

DNA-PK Ku80 mediated dimer bound to DNA polymerase Lambda and DNA ligase 4/XRCC4

Method: ELECTRON MICROSCOPY Dmax: 239.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 E； UniProt 1–911 Not recorded X-ray repair cross-complementing protein 5 × 1 （P13010） Protein PAXX × 1 （Q9BUH6） DNA repair protein XRCC4 × 2 （Q13426） DNA-dependent protein kinase catalytic subunit × 1 （P78527） X-ray repair cross-complementing protein 6 × 1 （P12956） DNA × 1 DNA × 1 DNA polymerase lambda × 1 （Q9UGP5） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.25 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 9GD7 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
9IAX DNA-PK, LX4, XLF - Catalytic domain of L4 Deposited 2025-02-11 Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain K 1–911（911 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
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 1
Chains and sequence ranges Author chain E； PDBConstruct 1–911； UniProt 1–911

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 L； UniProt 1–732 Not recorded DNA ligase 4 × 1 （P49917） Protein PAXX × 1 （Q9BUH6） DNA repair protein XRCC4 × 2 （Q13426） DNA-dependent protein kinase catalytic subunit × 1 （P78527） X-ray repair cross-complementing protein 6 × 1 （P12956） DNA × 1 DNA × 1 DNA polymerase lambda × 1 （Q9UGP5） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.25 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 9GD7 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 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 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
9GYF Ku70/80 with PAXX peptide mutation K193R Deposited 2024-10-02 Different oligomeric state Different ligand/ion 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
9IAX DNA-PK, LX4, XLF - Catalytic domain of L4 Deposited 2025-02-11 Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain C 1–732（732 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
9IGW Ku70/80 bound to 147 bp nucleosome Deposited 2025-02-20 Different 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 2
Chains and sequence ranges Author chain L； PDBConstruct 1–732； UniProt 1–732

Protein PAXX

Homo sapiens

UniProt Q9BUH6

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 M； UniProt 1–204 Not recorded DNA ligase 4 × 1 （P49917） X-ray repair cross-complementing protein 5 × 1 （P13010） DNA repair protein XRCC4 × 2 （Q13426） DNA-dependent protein kinase catalytic subunit × 1 （P78527） X-ray repair cross-complementing protein 6 × 1 （P12956） DNA × 1 DNA × 1 DNA polymerase lambda × 1 （Q9UGP5） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.25 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 9GD7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3WTD Structure of PAXX Deposited 2014-04-09 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 1–166（166 aa） Fragment：N-terminal domain, UNP RESIDUES 1-166
Chain B 1–166（166 aa） Fragment：N-terminal domain, UNP RESIDUES 1-166
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；1.5M ammonium sulfate, 12%(v/v) glycerol, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.35 Å R-free 0.229
3WTF Structure of PAXX Deposited 2014-04-09 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 1–204（204 aa）
Chain B 1–204（204 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；1M sodium malonate, 1% (v/v) 1,4-Dioxane, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.45 Å R-free 0.268
4WJA Crystal Structure of PAXX Deposited 2014-09-29 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 1–145（145 aa） Fragment：UNP RESIDUES 1-145
Chain B 1–145（145 aa） Fragment：UNP RESIDUES 1-145
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；289 K；2.24M Ammonium sulfate, 0.1M Bis-Tris, pH 5.5
Resolution 2.60 Å R-free 0.267
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 C 1–204（204 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 C 1–204（204 aa）
Not recorded PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.68 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 J 177–204（28 aa）
Chain T 177–204（28 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 D 1–204（204 aa）
Chain M 1–204（204 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 c 1–204（204 aa）
Chain i 1–204（204 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 D 1–204（204 aa）
Chain M 1–204（204 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
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 S 1–204（204 aa）
Chain T 1–204（204 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 S 1–204（204 aa）
Chain T 1–204（204 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 G 1–204（204 aa）
Chain H 1–204（204 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 G 1–204（204 aa）
Chain H 1–204（204 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 G 1–204（204 aa）
Chain H 1–204（204 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 structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain M 1–204（204 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
9GYF Ku70/80 with PAXX peptide mutation K193R Deposited 2024-10-02 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain C 180–202（23 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
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 G 1–204（204 aa）
Chain H 1–204（204 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 G 1–204（204 aa）
Chain H 1–204（204 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 G 1–204（204 aa）
Chain H 1–204（204 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

19 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAXX_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain M； PDBConstruct 1–204； UniProt 1–204

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 P； UniProt 1–336 Chain Q； UniProt 1–336 Not recorded DNA ligase 4 × 1 （P49917） X-ray repair cross-complementing protein 5 × 1 （P13010） Protein PAXX × 1 （Q9BUH6） DNA-dependent protein kinase catalytic subunit × 1 （P78527） X-ray repair cross-complementing protein 6 × 1 （P12956） DNA × 1 DNA × 1 DNA polymerase lambda × 1 （Q9UGP5） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.25 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 9GD7 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
9IAX DNA-PK, LX4, XLF - Catalytic domain of L4 Deposited 2025-02-11 Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain G 1–336（336 aa）
Chain H 1–336（336 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
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 4
Chains and sequence ranges Author chain P； PDBConstruct 1–336； UniProt 1–336 Author chain Q； PDBConstruct 1–336； UniProt 1–336

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 S； UniProt 1–4128 Not recorded DNA ligase 4 × 1 （P49917） X-ray repair cross-complementing protein 5 × 1 （P13010） Protein PAXX × 1 （Q9BUH6） DNA repair protein XRCC4 × 2 （Q13426） X-ray repair cross-complementing protein 6 × 1 （P12956） DNA × 1 DNA × 1 DNA polymerase lambda × 1 （Q9UGP5） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.25 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 9GD7 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 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 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
9IAX DNA-PK, LX4, XLF - Catalytic domain of L4 Deposited 2025-02-11 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 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 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 5
Chains and sequence ranges Author chain S； 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 T； UniProt 1–609 Not recorded DNA ligase 4 × 1 （P49917） X-ray repair cross-complementing protein 5 × 1 （P13010） Protein PAXX × 1 （Q9BUH6） DNA repair protein XRCC4 × 2 （Q13426） DNA-dependent protein kinase catalytic subunit × 1 （P78527） DNA × 1 DNA × 1 DNA polymerase lambda × 1 （Q9UGP5） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.25 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 9GD7 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 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 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
9GYF Ku70/80 with PAXX peptide mutation K193R Deposited 2024-10-02 Different oligomeric state Different ligand/ion 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
9IAX DNA-PK, LX4, XLF - Catalytic domain of L4 Deposited 2025-02-11 Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric
Chain B 1–609（609 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.97 Å
9IGW Ku70/80 bound to 147 bp nucleosome Deposited 2025-02-20 Different 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 6
Chains and sequence ranges Author chain T； PDBConstruct 1–609； UniProt 1–609

DNA polymerase lambda

Homo sapiens

UniProt Q9UGP5

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 1–575 Not recorded DNA ligase 4 × 1 （P49917） X-ray repair cross-complementing protein 5 × 1 （P13010） Protein PAXX × 1 （Q9BUH6） DNA repair protein XRCC4 × 2 （Q13426） DNA-dependent protein kinase catalytic subunit × 1 （P78527） X-ray repair cross-complementing protein 6 × 1 （P12956） DNA × 1 DNA × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.25 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 9GD7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NZP Solution Structure of the Lyase Domain of Human DNA Polymerase Lambda Deposited 2003-02-19 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 242–327（86 aa） Fragment：POLYMERASE LAMBDA LYASE DOMAIN(RESIDUES 242 - 327)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 5mM Tris, 100mM NaCl, 5mM NaN3；Pressure ambient
NMR sample composition 2mM pol lambda 8 kDa domain U-15N,13C; 5mM Tris-d11; 100mM NaCl; 1mM DTT; 5mM NaN3 | 90% H2O/10% D2O
Resolution not provided
1RZT Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule Deposited 2003-12-29 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 245–575（331 aa） Fragment：catalytic domain of polymerase lambda
Mutation：residues 245-575 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；279 K；cacodylate, sodium acetate, PEG8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.10 Å R-free 0.260
1RZT Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule Deposited 2003-12-29 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain E 245–575（331 aa） Fragment：catalytic domain of polymerase lambda
Mutation：residues 245-575 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；279 K；cacodylate, sodium acetate, PEG8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.10 Å R-free 0.260
1RZT Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule Deposited 2003-12-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain I 245–575（331 aa） Fragment：catalytic domain of polymerase lambda
Mutation：residues 245-575 NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；279 K；cacodylate, sodium acetate, PEG8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.10 Å R-free 0.260
1RZT Crystal structure of DNA polymerase lambda complexed with a two nucleotide gap DNA molecule Deposited 2003-12-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain M 245–575（331 aa） Fragment：catalytic domain of polymerase lambda
Mutation：residues 245-575 NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；279 K；cacodylate, sodium acetate, PEG8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Resolution 2.10 Å R-free 0.260
1XSL Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap Deposited 2004-10-19 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 242–575（334 aa） Fragment：39 kDa catalytic C-terminal domain
Not recorded MG MAGNESIUM ION × 1 CAC CACODYLATE ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；MPD, Cacodylate, sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.252
1XSL Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap Deposited 2004-10-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain E 242–575（334 aa） Fragment：39 kDa catalytic C-terminal domain
Not recorded MG MAGNESIUM ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；MPD, Cacodylate, sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.252
1XSL Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap Deposited 2004-10-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain I 242–575（334 aa） Fragment：39 kDa catalytic C-terminal domain
Not recorded NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；MPD, Cacodylate, sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.252
1XSL Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap Deposited 2004-10-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain M 242–575（334 aa） Fragment：39 kDa catalytic C-terminal domain
Not recorded NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；MPD, Cacodylate, sodium chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.252
1XSN Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap and ddTTP Deposited 2004-10-19 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa） Fragment：39 kDa catalytic C-terminal domain
Mutation：C543A EDO 1,2-ETHANEDIOL × 4 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Sodium Citrate, 2-propanol, sodium chloride, cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.255
1XSP Crystal Structure of human DNA polymerase lambda in complex with nicked DNA and pyrophosphate Deposited 2004-10-19 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa） Fragment：39 kDa catalytic C-terminal domain
Mutation：C543A NA SODIUM ION × 4 PPV PYROPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；2-propanol, sodium citrate, sodium chloride, cacodylate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.242
2BCQ DNA polymerase lambda in complex with a DNA duplex containing an unpaired Dtmp Deposited 2005-10-19 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 242–575（334 aa）
Not recorded NA SODIUM ION × 3 MG MAGNESIUM ION × 1 PPV PYROPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Sodium citrate, sodium cacodylate, 2-propanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.65 Å R-free 0.230
2BCR DNA polymerase lambda in complex with a DNA duplex containing an unpaired Damp Deposited 2005-10-19 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 242–575（334 aa）
Not recorded EDO 1,2-ETHANEDIOL × 5 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 PPV PYROPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Sodium citrate, sodium cacodylate, 2-propanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.75 Å R-free 0.231
2BCS DNA polymerase lambda in complex with a DNA duplex containing an unpaired Dcmp Deposited 2005-10-19 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 242–575（334 aa）
Not recorded MG MAGNESIUM ION × 1 NA SODIUM ION × 2 PPV PYROPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Sodium citrate, sodium cacodylate, 2-propanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.241
2BCU DNA polymerase lambda in complex with a DNA duplex containing an unpaired Damp and a T:T mismatch Deposited 2005-10-19 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 242–575（334 aa）
Not recorded NA SODIUM ION × 3 PPV PYROPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Sodium citrate, sodium cacodylate, 2-propanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.20 Å R-free 0.247
2BCV DNA polymerase lambda in complex with Dttp and a DNA duplex containing an unpaired Dtmp Deposited 2005-10-19 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 242–575（334 aa）
Not recorded MG MAGNESIUM ION × 1 NA SODIUM ION × 3 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；Sodium citrate, sodium cacodylate, 2-propanol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.00 Å R-free 0.232
2GWS Crystal Structure of human DNA Polymerase lambda with a G/G mismatch in the primer terminus Deposited 2006-05-05 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 242–575（334 aa）
Not recorded NA SODIUM ION × 3 CAC CACODYLATE ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；6% MPD, 50 mM Na Cacodylate, 100 mM NaCl, 50 mM MgCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.253
2GWS Crystal Structure of human DNA Polymerase lambda with a G/G mismatch in the primer terminus Deposited 2006-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain E 242–575（334 aa）
Not recorded NA SODIUM ION × 1 CAC CACODYLATE ION × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；6% MPD, 50 mM Na Cacodylate, 100 mM NaCl, 50 mM MgCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.253
2GWS Crystal Structure of human DNA Polymerase lambda with a G/G mismatch in the primer terminus Deposited 2006-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain I 242–575（334 aa）
Not recorded NA SODIUM ION × 1 CAC CACODYLATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；6% MPD, 50 mM Na Cacodylate, 100 mM NaCl, 50 mM MgCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.253
2GWS Crystal Structure of human DNA Polymerase lambda with a G/G mismatch in the primer terminus Deposited 2006-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain M 242–575（334 aa）
Not recorded NA SODIUM ION × 3 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；6% MPD, 50 mM Na Cacodylate, 100 mM NaCl, 50 mM MgCl2, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.253
2JW5 Polymerase Lambda BRCT domain Deposited 2007-10-05 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 34–135（102 aa） Fragment：BRCT domain (residues 34-135)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；283 K；Ionic strength (raw mmCIF value) 0.075；Pressure ambient
NMR sample composition 10 uM DSS, 25 mM TRIS, 75 mM sodium chloride, 1 mM [U-2H] DTT, 0.2 mM EDTA, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 10 uM DSS, 25 mM TRIS, 75 mM sodium chloride, 1 mM [U-2H] DTT, 0.2 mM EDTA, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2PFN Na in the active site of DNA Polymerase lambda Deposited 2007-04-05 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：C543A NA SODIUM ION × 5 MG MAGNESIUM ION × 1 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；278 K；10-20% 2-propanol, 0.2 M sodium citrate and 0.1M sodium cacodylate , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 1.90 Å R-free 0.232
2PFO DNA Polymerase lambda in complex with DNA and dUPNPP Deposited 2007-04-05 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：C543A MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 1 NA SODIUM ION × 4 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；278 K；10-20% 2-propanol, 0.2 M sodium citrate and 0.1M sodium cacodylate , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 2.00 Å R-free 0.242
2PFP DNA Polymerase lambda in complex with DNA and dCTP Deposited 2007-04-05 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：C543A NA SODIUM ION × 5 MG MAGNESIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；278 K；10-20% 2-propanol, 0.2 M sodium citrate and 0.1M sodium cacodylate , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 2.10 Å R-free 0.245
2PFQ Manganese promotes catalysis in a DNA polymerase lambda-DNA crystal Deposited 2007-04-05 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：C543A MG MAGNESIUM ION × 1 NA SODIUM ION × 2 MN MANGANESE (II) ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 PPV PYROPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；278 K；10-20% 2-propanol, 0.2 M sodium citrate and 0.1M sodium cacodylate , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Resolution 2.10 Å R-free 0.287
3C5F Structure of a binary complex of the R517A Pol lambda mutant Deposited 2008-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa） Fragment：DNA binding region
Mutation：R517A NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2M ammonium acetate, 100 mM Hepes, pH 7 and 10% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.25 Å R-free 0.263
3C5F Structure of a binary complex of the R517A Pol lambda mutant Deposited 2008-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 242–575（334 aa） Fragment：DNA binding region
Mutation：R517A NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2M ammonium acetate, 100 mM Hepes, pH 7 and 10% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.25 Å R-free 0.263
3C5G Structure of a ternary complex of the R517K Pol lambda mutant Deposited 2008-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa） Fragment：DNA binding region
Mutation：R517K MG MAGNESIUM ION × 1 NA SODIUM ION × 4 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1M KCl, 10 mM MgCl2, 50 mM Tris-HCl, pH 8.5 and 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.20 Å R-free 0.236
3C5G Structure of a ternary complex of the R517K Pol lambda mutant Deposited 2008-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 242–575（334 aa） Fragment：DNA binding region
Mutation：R517K MG MAGNESIUM ION × 1 NA SODIUM ION × 4 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.1M KCl, 10 mM MgCl2, 50 mM Tris-HCl, pH 8.5 and 30% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.20 Å R-free 0.236
3HW8 ternary complex of DNA polymerase lambda of a two nucleotide gapped DNA substrate with a C in the scrunch site Deposited 2009-06-17 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa） Fragment：UNP residues 242-575, 39 kDa catalytic domain
Mutation：C543A MG MAGNESIUM ION × 1 NA SODIUM ION × 4 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；2M sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.233
3HWT Ternary complex of DNA polymerase lambda bound to a two nucleotide gapped DNA substrate with a scrunched dA Deposited 2009-06-18 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa） Fragment：UNP residues 242-575
Mutation：C543A D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；277 K；19% 2-propanol, ).1 M Na Cacodylate, pH 5.5, Na Citrate 0.2M, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.261
3HX0 ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched dA Deposited 2009-06-19 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa） Fragment：UNP residues 242-575, Catalytic domain
Mutation：L277A, H511A, R514A ,C543A D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；5% 2-propanol, 25mM ammonium acetate, 15mM magnesium acetate, 100mM cacodylic acid., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.268
3HX0 ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched dA Deposited 2009-06-19 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain F 242–575（334 aa） Fragment：UNP residues 242-575, Catalytic domain
Mutation：L277A, H511A, R514A ,C543A D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；5% 2-propanol, 25mM ammonium acetate, 15mM magnesium acetate, 100mM cacodylic acid., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.268
3HX0 ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched dA Deposited 2009-06-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain K 242–575（334 aa） Fragment：UNP residues 242-575, Catalytic domain
Mutation：L277A, H511A, R514A ,C543A D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；5% 2-propanol, 25mM ammonium acetate, 15mM magnesium acetate, 100mM cacodylic acid., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.268
3HX0 ternary complex of L277A, H511A, R514 mutant pol lambda bound to a 2 nucleotide gapped DNA substrate with a scrunched dA Deposited 2009-06-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain P 242–575（334 aa） Fragment：UNP residues 242-575, Catalytic domain
Mutation：L277A, H511A, R514A ,C543A D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；5% 2-propanol, 25mM ammonium acetate, 15mM magnesium acetate, 100mM cacodylic acid., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.268
3MDA DNA polymerase lambda in complex with araC Deposited 2010-03-30 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 252–575（324 aa）
Not recorded PPV PYROPHOSPHATE × 1 NA SODIUM ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 5.5；277 K；2-propanol, pH 5.5, hanging drop, temperature 277K
Resolution 2.03 Å R-free 0.259
3MDC DNA polymerase lambda in complex with dFdCTP Deposited 2010-03-30 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 252–575（324 aa）
Not recorded GTF 2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate) × 1 NA SODIUM ION × 4 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 5.5；277 K；2-propanol, pH 5.5, hanging drop, temperature 277K
Resolution 2.00 Å R-free 0.266
3MGH Binary complex of a DNA polymerase lambda loop mutant Deposited 2010-04-06 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–462（221 aa） Fragment：Loop mutant of DNA polymerase lambda
Chain A 472–575（104 aa） Fragment：Loop mutant of DNA polymerase lambda
Mutation：SQEENGQQQ to KGET Mutation：SQEENGQQQ to KGET NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；277 K；2-propanol, pH 6.5, hanging drop, temperature 277K
Resolution 2.40 Å R-free 0.261
3MGH Binary complex of a DNA polymerase lambda loop mutant Deposited 2010-04-06 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain C 242–462（221 aa） Fragment：Loop mutant of DNA polymerase lambda
Chain C 472–575（104 aa） Fragment：Loop mutant of DNA polymerase lambda
Mutation：SQEENGQQQ to KGET Mutation：SQEENGQQQ to KGET NA SODIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 6.5；277 K；2-propanol, pH 6.5, hanging drop, temperature 277K
Resolution 2.40 Å R-free 0.261
3MGI Ternary complex of a DNA polymerase lambda loop mutant Deposited 2010-04-06 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–462（221 aa） Fragment：Loop mutant of DNA polymerase lambda
Chain A 472–575（104 aa） Fragment：Loop mutant of DNA polymerase lambda
Mutation：SQEENGQQQ to KGET Mutation：SQEENGQQQ to KGET D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions hanging drop；pH 5.5；277 K；2-propanol, pH 5.5, hanging drop, temperature 277K
Resolution 2.60 Å R-free 0.270
3PML crystal structure of a polymerase lambda variant with a dGTP analog opposite a templating T Deposited 2010-11-17 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 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded 1GC 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；.1M NaCl, 0.1M Hepes pH 7.5 and 10%PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.60 Å R-free 0.271
3PML crystal structure of a polymerase lambda variant with a dGTP analog opposite a templating T Deposited 2010-11-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded 1GC 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；.1M NaCl, 0.1M Hepes pH 7.5 and 10%PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.60 Å R-free 0.271
3PMN ternary crystal structure of polymerase lambda variant with a GT mispair at the primer terminus with Mn2+ in the active site Deposited 2010-11-17 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 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded 1GC 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine × 1 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 3 NA SODIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；2M formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.20 Å R-free 0.243
3PNC Ternary crystal structure of a polymerase lambda variant with a GT mispair at the primer terminus and sodium at catalytic metal site Deposited 2010-11-18 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 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded 1GC 2'-deoxy-5'-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]guanosine × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；277 K；2M formate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.00 Å R-free 0.236
3UPQ Crystal structure of the pre-catalytic ternary complex of polymerase lambda with an rATP analog opposite a templating T. Deposited 2011-11-18 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa） Fragment：Loop mutant of DNA polymerase lambda
Mutation：SQEENGQQQ to KGET ZAN 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 1 MN MANGANESE (II) ION × 3 NA SODIUM ION × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100mM Na HEPES pH 7.5, 1.0M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.95 Å R-free 0.244
3UQ0 Crystal structure of the post-catalytic product complex of polymerase lambda with an rAMP at the primer terminus. Deposited 2011-11-18 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa） Fragment：Loop mutant of DNA polymerase lambda
Mutation：SQEENGQQQ to KGET NA SODIUM ION × 1 SO4 SULFATE ION × 3 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；100mM Na HEPES pH 7.5, 1.0M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.14 Å R-free 0.239
3UQ2 Crystal structure of the post-catalytic product complex of polymerase lambda with an rCMP inserted opposite a templating G and dAMP inserted opposite a templating T at the primer terminus. Deposited 2011-11-18 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa） Fragment：Loop mutant of DNA polymerase lambda
Mutation：SQEENGQQQ to KGET PPV PYROPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；170mM ammonium acetate, 85mM sodium citrate tribasic dihydrate pH 5.6, 25.5% (w/v) PEG4000, 15% (v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.25 Å R-free 0.254
4FO6 Crystal structure of the pre-catalytic ternary complex of polymerase lambda with a dATP analog opposite a templating T and an rCMP at the primer terminus. Deposited 2012-06-20 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 Monomer；Protein × 1 PDB declaration: hexameric
Chain A 242–575（334 aa） Fragment：Loop mutant of DNA polymerase lambda
Mutation：SQEENGQQQ to KGET MG MAGNESIUM ION × 1 NA SODIUM ION × 2 CL CHLORIDE ION × 1 MN MANGANESE (II) ION × 1 F2A 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50mM MES pH 6.5, 9%(v/v) PEG400, 100mM KCL, 10mM MGCL2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.01 Å R-free 0.231
4K4G Ternary crystal structures of human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND L-DCTP. Deposited 2013-04-12 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 245–575（331 aa）
Not recorded 1S0 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one × 1 CA CALCIUM ION × 6 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.15 Å R-free 0.250
4K4G Ternary crystal structures of human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND L-DCTP. Deposited 2013-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain E 245–575（331 aa）
Not recorded 1S0 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one × 1 CA CALCIUM ION × 6 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.15 Å R-free 0.250
4K4G Ternary crystal structures of human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND L-DCTP. Deposited 2013-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain I 245–575（331 aa）
Not recorded 1S0 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one × 1 CA CALCIUM ION × 6 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.15 Å R-free 0.250
4K4G Ternary crystal structures of human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND L-DCTP. Deposited 2013-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain M 245–575（331 aa）
Not recorded 1S0 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one × 1 CA CALCIUM ION × 4 ACT ACETATE ION × 1 CAC CACODYLATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000 , pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.15 Å R-free 0.250
4K4H Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)3TC-TP. Deposited 2013-04-12 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 245–575（331 aa）
Not recorded 1RZ Lamivudine Triphosphate × 1 CA CALCIUM ION × 7 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.260
4K4H Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)3TC-TP. Deposited 2013-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain E 245–575（331 aa）
Not recorded 1RZ Lamivudine Triphosphate × 1 CA CALCIUM ION × 5 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.260
4K4H Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)3TC-TP. Deposited 2013-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain I 245–575（331 aa）
Not recorded 1RZ Lamivudine Triphosphate × 1 CA CALCIUM ION × 5 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.260
4K4H Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)3TC-TP. Deposited 2013-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain M 245–575（331 aa）
Not recorded 1RZ Lamivudine Triphosphate × 1 CA CALCIUM ION × 6 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.260
4K4I Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)FTC-TP. Deposited 2013-04-12 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 245–575（331 aa）
Not recorded 1RY [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 CA CALCIUM ION × 7 ACT ACETATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.25 Å R-free 0.274
4K4I Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)FTC-TP. Deposited 2013-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain E 245–575（331 aa）
Not recorded 1RY [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 CA CALCIUM ION × 6 ACT ACETATE ION × 2 CAC CACODYLATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.25 Å R-free 0.274
4K4I Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)FTC-TP. Deposited 2013-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain I 245–575（331 aa）
Not recorded 1RY [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 CA CALCIUM ION × 5 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.25 Å R-free 0.274
4K4I Ternary crystal structures of a human DNA POLYMERASE LAMBDA IN COMPLEX WITH DNA AND (-)FTC-TP. Deposited 2013-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain M 245–575（331 aa）
Not recorded 1RY [[(2R,5S)-5-(4-azanyl-5-fluoranyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate × 1 CA CALCIUM ION × 5 ACT ACETATE ION × 1 CAC CACODYLATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.1 M SODIUM CACODYLATE, 0.2 M CALCIUM ACETATE, 4% PEG 8000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.25 Å R-free 0.274
4X5V Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating A and incorporated 8-oxo-dGMP Deposited 2014-12-05 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 251–575（325 aa）
Not recorded NA SODIUM ION × 1 MG MAGNESIUM ION × 1 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；0.1 M sodium citrate pH 5.6 and 1 M ammonium phosphate monobasic
Resolution 2.15 Å R-free 0.245
4XA5 Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating A and an incoming 8-oxo-dGTP Deposited 2014-12-12 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 251–575（325 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 8DG 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ACT ACETATE ION × 3 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；0.1 M sodium cacodylate trihydrate pH 7.4 and 1.9 M sodium acetate trihydrate
Resolution 1.90 Å R-free 0.227
4XQ8 Human DNA polymerase lambda- MgdATP binary complex and complex with 6 paired DNA Deposited 2015-01-19 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；0.1 M Lithium Sulfate monohydrate, 0.1 M HEPES-Sodium, 0.1 M Potassium Sodium Tartrate
Resolution 2.80 Å R-free 0.240
4XQ8 Human DNA polymerase lambda- MgdATP binary complex and complex with 6 paired DNA Deposited 2015-01-19 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 A 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；0.1 M Lithium Sulfate monohydrate, 0.1 M HEPES-Sodium, 0.1 M Potassium Sodium Tartrate
Resolution 2.80 Å R-free 0.240
4XRH Human DNA polymerase lambda- MgdTTP binary and complex with 6 paired DNA Deposited 2015-01-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Resolution 3.00 Å R-free 0.251
4XRH Human DNA polymerase lambda- MgdTTP binary and complex with 6 paired DNA Deposited 2015-01-21 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 A 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded MG MAGNESIUM ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Resolution 3.00 Å R-free 0.251
4XUS Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating A and an incoming dTTP Deposited 2015-01-26 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 251–575（325 aa） Fragment：UNP residues 251-575
Not recorded TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；0.1 M sodium acetate trihydrate 2.0 M sodium formate
Resolution 2.40 Å R-free 0.236
5CA7 Human DNA polymerase lambda- MgdGTP binary and complex with 6 paired DNA Deposited 2015-06-29 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Resolution 2.52 Å R-free 0.246
5CA7 Human DNA polymerase lambda- MgdGTP binary and complex with 6 paired DNA Deposited 2015-06-29 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 A 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Resolution 2.52 Å R-free 0.246
5CB1 Apo enzyme of human Polymerase lambda Deposited 2015-06-30 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 250–575（326 aa） Fragment：UNP residues 250-575
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M HEPES, 3.0M Sodium Chloride
Resolution 3.30 Å R-free 0.264
5CB1 Apo enzyme of human Polymerase lambda Deposited 2015-06-30 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 250–575（326 aa） Fragment：UNP residues 250-575
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M HEPES, 3.0M Sodium Chloride
Resolution 3.30 Å R-free 0.264
5CHG Human DNA polymerase lambda L431A mutant- MgdGTP binary and complex with 6 paired DNA Deposited 2015-07-10 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 Monomer；Protein × 1 PDB declaration: trimeric
Chain A 242–575（334 aa） Fragment：UNP residues 242-575
Mutation：L431A MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Resolution 2.90 Å R-free 0.247
5CHG Human DNA polymerase lambda L431A mutant- MgdGTP binary and complex with 6 paired DNA Deposited 2015-07-10 Different construct Different mutation/modification 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 242–575（334 aa） Fragment：UNP residues 242-575
Mutation：L431A MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 DGT 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Resolution 2.90 Å R-free 0.247
5CJ7 Human DNA polymerase lambda L431A mutant- MgdTTP binary and complex with 6 paired DNA Deposited 2015-07-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 242–575（334 aa） Fragment：UNP residues 242-575
Mutation：L431A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Resolution 2.90 Å R-free 0.258
5CJ7 Human DNA polymerase lambda L431A mutant- MgdTTP binary and complex with 6 paired DNA Deposited 2015-07-14 Different construct Different mutation/modification 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 242–575（334 aa） Fragment：UNP residues 242-575
Mutation：L431A MG MAGNESIUM ION × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Resolution 2.90 Å R-free 0.258
5CP2 Human DNA polymerase lambda L431A mutant- Apoenzyme and complex with 6 paired DNA Deposited 2015-07-21 Different construct Different mutation/modification 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 242–575（334 aa） Fragment：UNP residues 242-575
Mutation：L431A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Resolution 2.36 Å R-free 0.238
5CP2 Human DNA polymerase lambda L431A mutant- Apoenzyme and complex with 6 paired DNA Deposited 2015-07-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain B 242–575（334 aa） Fragment：UNP residues 242-575
Mutation：L431A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Resolution 2.36 Å R-free 0.238
5CR0 Human DNA polymerase lambda L431A mutant- MgdCTP binary and complex with 6 paired DNA Deposited 2015-07-22 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric
Chain A 242–575（334 aa） Fragment：UNP residues 242-575
Mutation：L431A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Resolution 2.75 Å R-free 0.281
5CR0 Human DNA polymerase lambda L431A mutant- MgdCTP binary and complex with 6 paired DNA Deposited 2015-07-22 Different construct Different mutation/modification 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 242–575（334 aa） Fragment：UNP residues 242-575
Mutation：L431A MG MAGNESIUM ION × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Resolution 2.75 Å R-free 0.281
5CWR Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one nucleotide DNA gap and dCTP Deposited 2015-07-28 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 250–575（326 aa） Fragment：UNP residues 250-575
Mutation：L431A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.15 M Potassium Bromide, 30% Polyethylene Glycol Monomethyl ether 2000
Resolution 2.50 Å R-free 0.234
5CWR Crystal Structure of human DNA polymerase lambda L431A mutant in complex with a one nucleotide DNA gap and dCTP Deposited 2015-07-28 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 250–575（326 aa） Fragment：UNP residues 250-575
Mutation：L431A DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.15 M Potassium Bromide, 30% Polyethylene Glycol Monomethyl ether 2000
Resolution 2.50 Å R-free 0.234
5DDM Human DNA polymerase lambda- Apoenzyme and complex with 6 paired DNA Deposited 2015-08-25 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: trimeric
Chain B 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Resolution 2.80 Å R-free 0.239
5DDM Human DNA polymerase lambda- Apoenzyme and complex with 6 paired DNA Deposited 2015-08-25 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 A 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M Lithium Sulfate monohydrate, 0.1M HEPES-Sodium, 0.1M Potassium Sodium Tartrate
Resolution 2.80 Å R-free 0.239
5DDY Binary complex of human Polymerase lambda with dCTP Deposited 2015-08-25 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 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M HEPES, 3.0M Sodium Chloride
Resolution 3.36 Å R-free 0.297
5DDY Binary complex of human Polymerase lambda with dCTP Deposited 2015-08-25 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 C 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M HEPES, 3.0M Sodium Chloride
Resolution 3.36 Å R-free 0.297
5DDY Binary complex of human Polymerase lambda with dCTP Deposited 2015-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain E 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M HEPES, 3.0M Sodium Chloride
Resolution 3.36 Å R-free 0.297
5DDY Binary complex of human Polymerase lambda with dCTP Deposited 2015-08-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain G 242–575（334 aa） Fragment：UNP residues 242-575
Not recorded MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1M HEPES, 3.0M Sodium Chloride
Resolution 3.36 Å R-free 0.297
5DKW Ternary crystal structure of polymerase lambda with a GA mispair at the primer terminus with Ca2+ in the active Deposited 2015-09-04 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 249–575（327 aa） Fragment：UNP residues 249-575
Not recorded DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, 30%(v/v) Jeffamine ED-2100 Reagent
Resolution 2.69 Å R-free 0.233
5DKW Ternary crystal structure of polymerase lambda with a GA mispair at the primer terminus with Ca2+ in the active Deposited 2015-09-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 249–575（327 aa） Fragment：UNP residues 249-575
Not recorded DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.1 M HEPES, 30%(v/v) Jeffamine ED-2100 Reagent
Resolution 2.69 Å R-free 0.233
5III Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating 8-oxo-dG and an incoming dATP Deposited 2016-03-01 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 242–575（334 aa）
Not recorded DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 NA SODIUM ION × 2 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 1.80 Å R-free 0.225
5IIJ Crystal structure of the pre-catalytic ternary complex of DNA polymerase lambda with a templating 8-oxo-dG and an incoming dCTP Deposited 2016-03-01 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 242–575（334 aa）
Not recorded DCT 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium cacodylate pH 7.0 and 1.0 M sodium acetate trihydrate
Resolution 1.72 Å R-free 0.224
5IIK Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating 8-oxo-dG and incorporated dC Deposited 2016-03-01 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 242–575（334 aa）
Not recorded CIT CITRIC ACID × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；0.2 M ammonium acetate, 0.1 M sodium citrate pH 4.8, and 2-7% PEG 4000
Resolution 1.98 Å R-free 0.238
5IIL Crystal structure of the post-catalytic nick complex of DNA polymerase lambda with a templating 8-oxo-dG and incorporated dA Deposited 2016-03-01 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 242–575（334 aa）
Not recorded CIT CITRIC ACID × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；0.2 M ammonium acetate, 0.1 M sodium citrate pH 4.8, and 3-5% PEG 4000
Resolution 1.96 Å R-free 0.217
5IIM Crystal structure of the pre-catalytic ternary extension complex of DNA polymerase lambda with an 8-oxo-dG:dA base-pair Deposited 2016-03-01 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 242–575（334 aa）
Not recorded DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；0.2 M ammonium acetate, 0.1 M sodium citrate pH 4.8, and 3-5% PEG 4000
Resolution 1.94 Å R-free 0.216
5IIN Crystal structure of the pre-catalytic ternary extension complex of DNA polymerase lambda with an 8-oxo-dG:dC base-pair Deposited 2016-03-01 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 242–575（334 aa）
Not recorded DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 NA SODIUM ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；0.2 M ammonium acetate, 0.1 M sodium citrate pH 4.8, and 3-5% PEG 4000
Resolution 2.15 Å R-free 0.231
5IIO Crystal structure of the DNA polymerase lambda binary complex Deposited 2016-03-01 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 242–575（334 aa）
Not recorded NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；0.1 M KCl, 0.01 M CaCl2, 0.05 M HEPES pH 7.0, and 10% PEG 400
Resolution 2.08 Å R-free 0.235
5IIO Crystal structure of the DNA polymerase lambda binary complex Deposited 2016-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain E 242–575（334 aa）
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；0.1 M KCl, 0.01 M CaCl2, 0.05 M HEPES pH 7.0, and 10% PEG 400
Resolution 2.08 Å R-free 0.235
5IIO Crystal structure of the DNA polymerase lambda binary complex Deposited 2016-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain I 242–575（334 aa）
Not recorded NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；0.1 M KCl, 0.01 M CaCl2, 0.05 M HEPES pH 7.0, and 10% PEG 400
Resolution 2.08 Å R-free 0.235
5IIO Crystal structure of the DNA polymerase lambda binary complex Deposited 2016-03-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain M 242–575（334 aa）
Not recorded NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；278 K；0.1 M KCl, 0.01 M CaCl2, 0.05 M HEPES pH 7.0, and 10% PEG 400
Resolution 2.08 Å R-free 0.235
5W4G Importin binding to NLS peptide of DNA polymerase lambda Deposited 2017-06-10 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 4–32（29 aa）
Not recorded SO4 SULFATE ION × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M Bis Tris Propane 1.4 M Ammonium Sulfate
Resolution 2.04 Å R-free 0.200
7M07 Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate and incoming dUMPNPP Deposited 2021-03-10 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 234–575（342 aa）
Not recorded DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 5 CL CHLORIDE ION × 2 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；37.5mM Na cacodylate pH 6.5, 150mM KCl, 75mM magnesium acetate, 7.5% (w/v) PEG 8000
Resolution 1.57 Å R-free 0.188
7M08 Post-catalytic nicked complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate and incoming dUMPNPP Deposited 2021-03-10 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 234–575（342 aa）
Not recorded NA SODIUM ION × 3 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；37.5mM Na cacodylate pH 6.5, 150mM KCl, 75mM magnesium acetate, 7.5% (w/v) PEG8000
Resolution 1.70 Å R-free 0.209
7M09 Pre-catalytic quaternary complex of DNA Polymerase Lambda with blunt-ended DSB substrate and incoming dUMPNPP Deposited 2021-03-10 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: pentameric
Chain A 234–575（342 aa）
Not recorded DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 3 CL CHLORIDE ION × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；80mM Na cacodylate pH 6.5, 0.16mM calcium acetate, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol
Resolution 1.65 Å R-free 0.186
7M0A Incomplete in crystallo incorporation by DNA Polymerase Lambda bound to blunt-ended DSB substrate and incoming dTTP Deposited 2021-03-10 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: pentameric
Chain A 234–575（342 aa）
Not recorded TTP THYMIDINE-5'-TRIPHOSPHATE × 1 PPV PYROPHOSPHATE × 1 MG MAGNESIUM ION × 2 CA CALCIUM ION × 1 NA SODIUM ION × 3 CL CHLORIDE ION × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；80mM Na cacodylate pH 6.5, 0.16M calcium acetate, 14.4% (w/v) PEG 8000, 20% (v/v) glycerol
Resolution 1.83 Å R-free 0.193
7M0B Pre-catalytic quaternary complex of DNA Polymerase Lambda with bound mismatched DSB and incoming dUMPNPP Deposited 2021-03-10 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: pentameric
Chain A 234–575（342 aa）
Not recorded DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 4 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；76.5mM Na cacodylate pH 6.5, 0.153M ammonium sulfate, 22.95% (w/v) PEG8000, 13.5% (v/v) glycerol, 0.2M NDSB-201
Resolution 2.00 Å R-free 0.200
7M0C Post-catalytic nicked complex of DNA Polymerase Lambda with bound mismatched DSB substrate Deposited 2021-03-10 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: pentameric
Chain A 234–575（342 aa）
Not recorded MG MAGNESIUM ION × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 2 PPV PYROPHOSPHATE × 1 SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；76.5mM Na cacodylate pH 6.5, 0.153M ammonium sulfate, 22.95% (w/v) PEG 8000, 13.5% (v/v) glycerol, 0.2M NDSB-201
Resolution 2.65 Å R-free 0.229
7M0D Pre-catalytic quaternary complex of DNA Polymerase Lambda with bound complementary DSB substrate and incoming dUMPNPP Deposited 2021-03-10 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: pentameric
Chain A 234–575（342 aa）
Not recorded DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 NA SODIUM ION × 2 MG MAGNESIUM ION × 1 K POTASSIUM ION × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.192M tri-potassium citrate, 18.8% (w/v) PEG 3350
Resolution 1.80 Å R-free 0.189
7M0D Pre-catalytic quaternary complex of DNA Polymerase Lambda with bound complementary DSB substrate and incoming dUMPNPP Deposited 2021-03-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric
Chain B 234–575（342 aa）
Not recorded DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 NA SODIUM ION × 3 MG MAGNESIUM ION × 1 K POTASSIUM ION × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1 FMT FORMIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.192M tri-potassium citrate, 18.8% (w/v) PEG 3350
Resolution 1.80 Å R-free 0.189
7M0E Pre-catalytic synaptic complex of DNA Polymerase Lambda with gapped DSB substrate and incoming dUMPNPP Deposited 2021-03-10 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 232–575（344 aa）
Not recorded DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.138M sodium sulfate, 20% (w/v) PEG 3350
Resolution 2.25 Å R-free 0.222
7M0E Pre-catalytic synaptic complex of DNA Polymerase Lambda with gapped DSB substrate and incoming dUMPNPP Deposited 2021-03-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain B 232–575（344 aa）
Not recorded DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.138M sodium sulfate, 20% (w/v) PEG 3350
Resolution 2.25 Å R-free 0.222
7M0E Pre-catalytic synaptic complex of DNA Polymerase Lambda with gapped DSB substrate and incoming dUMPNPP Deposited 2021-03-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain C 232–575（344 aa）
Not recorded DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.138M sodium sulfate, 20% (w/v) PEG 3350
Resolution 2.25 Å R-free 0.222
7M0E Pre-catalytic synaptic complex of DNA Polymerase Lambda with gapped DSB substrate and incoming dUMPNPP Deposited 2021-03-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein–DNA Monomer；Protein × 1 PDB declaration: tetrameric
Chain D 232–575（344 aa）
Not recorded DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.138M sodium sulfate, 20% (w/v) PEG 3350
Resolution 2.25 Å R-free 0.222
7M43 DNA Polymerase Lambda, TTP:At Ca2+ Ground State Ternary Complex Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：Loop1, C543A CA CALCIUM ION × 1 NA SODIUM ION × 5 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.98 Å R-free 0.231
7M44 DNA Polymerase Lambda, TTP:At Mg2+ Reaction State Ternary Complex, 90 sec Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：loop1, C543A TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 3 PPV PYROPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.90 Å R-free 0.226
7M45 DNA Polymerase Lambda, TTP:At Mg2+ Reaction State Ternary Complex, 120 sec Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：loop1, C543A PPV PYROPHOSPHATE × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 4 EDO 1,2-ETHANEDIOL × 1 SRT S,R MESO-TARTARIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.89 Å R-free 0.242
7M46 DNA Polymerase Lambda, TTP:At Mg2+ Product State Ternary Complex, 5 min Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：loop1, C543A MG MAGNESIUM ION × 1 NA SODIUM ION × 4 EDO 1,2-ETHANEDIOL × 4 PPV PYROPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.92 Å R-free 0.216
7M47 DNA Polymerase Lambda, TTP:At Mg2+ Product State Ternary Complex, 60 min Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：loop1, C543A SRT S,R MESO-TARTARIC ACID × 1 NA SODIUM ION × 4 MG MAGNESIUM ION × 1 PPV PYROPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.65 Å R-free 0.208
7M48 DNA Polymerase Lambda, TTP:At Mg2+ Product State Ternary Complex, 960 min Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：loop1, C543A NA SODIUM ION × 4 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 5 OXL OXALATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.93 Å R-free 0.220
7M49 DNA Polymerase Lambda, TTP:At Mn2+ Reaction State Ternary Complex, 5 min Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：loop1, C543A NA SODIUM ION × 3 MN MANGANESE (II) ION × 4 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 PPV PYROPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.60 Å R-free 0.216
7M4A DNA Polymerase Lambda, TTP:At Mn2+ Product State Ternary Complex, 20 min Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：loop1, C543A PPV PYROPHOSPHATE × 1 MN MANGANESE (II) ION × 4 NA SODIUM ION × 3 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.87 Å R-free 0.220
7M4B DNA Polymerase Lambda, TTP:At Mn2+ Product State Ternary Complex, 60 min Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：loop1, C543A MN MANGANESE (II) ION × 4 NA SODIUM ION × 3 PPV PYROPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.66 Å R-free 0.202
7M4C DNA Polymerase Lambda, TTP:At Mn2+ Product State Ternary Complex, 960 min Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：C543A PPV PYROPHOSPHATE × 1 MN MANGANESE (II) ION × 3 NA SODIUM ION × 3 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.95 Å R-free 0.214
7M4D DNA Polymerase Lambda, dCTP:At Ca2+ Ground State Ternary Complex Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：C543A CA CALCIUM ION × 1 NA SODIUM ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.82 Å R-free 0.254
7M4E DNA Polymerase Lambda, dCTP:At Mg2+ Reaction State Ternary Complex, 120 min Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：C543A PPV PYROPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 2 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.90 Å R-free 0.233
7M4F DNA Polymerase Lambda, dCTP:At Mg2+ Product State Ternary Complex, 300 min Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：C543A NA SODIUM ION × 3 MG MAGNESIUM ION × 1 PPV PYROPHOSPHATE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.95 Å R-free 0.241
7M4G DNA Polymerase Lambda, dCTP:At Mg2+ Product State Ternary Complex, 960 min Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：C543A NA SODIUM ION × 3 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 4 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.88 Å R-free 0.239
7M4H DNA Polymerase Lambda, dCTP:At Mn2+ Reaction State Ternary Complex, 225 min Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：C543A MN MANGANESE (II) ION × 3 NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 2 PPV PYROPHOSPHATE × 1 DCP 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.92 Å R-free 0.228
7M4I DNA Polymerase Lambda, dCTP:At Mn2+ Product State Ternary Complex, 420 min Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：C543A MN MANGANESE (II) ION × 3 NA SODIUM ION × 3 PPV PYROPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 2.00 Å R-free 0.247
7M4J DNA Polymerase Lambda, dCTP:At Mn2+ Product State Ternary Complex, 960 min Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：C543A MN MANGANESE (II) ION × 2 NA SODIUM ION × 3 PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 2.38 Å R-free 0.261
7M4K DNA Polymerase Lambda, TTPaS:At Ca2+ Ground State Ternary Complex Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：C543A CA CALCIUM ION × 1 NA SODIUM ION × 4 EDO 1,2-ETHANEDIOL × 6 YQS [[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methoxy-sulfanyl-phosphoryl] phosphono hydrogen phosphate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.72 Å R-free 0.227
7M4L DNA Polymerase Lambda, TTPaS:At Mn2+ Product State Ternary Complex, 60 min Deposited 2021-03-21 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–575（334 aa）
Mutation：C543A MN MANGANESE (II) ION × 3 NA SODIUM ION × 2 PPV PYROPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 1.70 Å R-free 0.215
7UN7 DNA Polymerase lambda in complex with a 1nt microhomology substrate Deposited 2022-04-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: pentameric
Chain A 242–575（334 aa）
Mutation：C543A TTP THYMIDINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 1 NA SODIUM ION × 2 CA CALCIUM ION × 2 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；80-95mM BICINE pH 8.3, 0.3M Na-K Tartrate, 18-22.5% PolyPure PEG
Resolution 2.04 Å R-free 0.247
8U0O Synaptic complex of human DNA polymerase Lambda DL variant engaged on a DNA double-strand break containing an unpaired 3' primer terminus Deposited 2023-08-29 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 Monomer；Protein × 1 PDB declaration: trimeric
Chain A 234–575（342 aa）
Mutation：Ser463-Gln471 deletion and replacement with KGET NA SODIUM ION × 1 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；0.1 M ADA pH 6.5, 1 M ammonium phosphate dibasic
Resolution 2.05 Å R-free 0.259
8U0P Synaptic complex of human DNA polymerase Lambda DL variant engaged on a noncomplementary DNA double-strand break Deposited 2023-08-29 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 234–464（231 aa）
Chain A 472–575（104 aa）
Mutation：Glu465-Gln471 deletion and replacement with single glycine Mutation：Glu465-Gln471 deletion and replacement with single glycine MG MAGNESIUM ION × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 4 SO4 SULFATE ION × 1 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；85 mM Na cacodylate pH 6.5, 0.17 M ammonium sulfate, 25.5 % (w/v) PEG 8000, 15% (v/v) glycerol
Resolution 1.90 Å R-free 0.193
9EWB DNA Polymerase Lambda I493R, TTP:At Ca2+ Ground State Ternary Complex Deposited 2024-04-03 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–462（221 aa）
Chain A 472–575（104 aa）
Mutation：I493R Mutation：I493R CA CALCIUM ION × 1 NA SODIUM ION × 2 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；20 mM bicine pH 7,5, 300 mM Na-K tartrate, 22,5% PEG Smear high
Resolution 2.32 Å R-free 0.225
9EWC DNA Polymerase Lambda I493R 528-530 NEY, TTP:At Ca2+ Ground State Ternary Complex Deposited 2024-04-03 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–462（221 aa）
Chain A 472–575（104 aa）
Mutation：I493R,[528-530] NEY Mutation：I493R,[528-530] NEY NA SODIUM ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；20 mM bicine pH 7.5 300 mM Na-K tartrate 20% PEG 1000
Resolution 3.67 Å R-free 0.293
9EWC DNA Polymerase Lambda I493R 528-530 NEY, TTP:At Ca2+ Ground State Ternary Complex Deposited 2024-04-03 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain C 242–462（221 aa）
Chain C 472–575（104 aa）
Mutation：I493R,[528-530] NEY Mutation：I493R,[528-530] NEY NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；20 mM bicine pH 7.5 300 mM Na-K tartrate 20% PEG 1000
Resolution 3.67 Å R-free 0.293
9EWD DNA Polymerase Lambda I493K E529D, TMP:At Ca2+ Ground State Ternary Complex Deposited 2024-04-03 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–462（221 aa）
Chain A 472–575（104 aa）
Not recorded TMP THYMIDINE-5'-PHOSPHATE × 1 NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 1 K POTASSIUM ION × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；20 mM bicine pH7.5 300 mM Na-K tartrate 20% PEG 20K
Resolution 2.12 Å R-free 0.245
9EWE DNA Polymerase Lambda I493K, E529D, Ca2+ Ground State Ternary Complex Deposited 2024-04-03 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–462（221 aa）
Chain A 472–575（104 aa）
Not recorded CA CALCIUM ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；20 mM bicine pH7.5 300 mM Na-K tartrate 14% PEG 10K
Resolution 3.04 Å R-free 0.279
9EWG DNA Polymerase Lambda I493K, TTP:At Ca2+ Ground State Ternary Complex Deposited 2024-04-03 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 Monomer；Protein × 1 PDB declaration: tetrameric
Chain A 242–462（221 aa）
Chain A 472–575（104 aa）
Not recorded NA SODIUM ION × 3 EDO 1,2-ETHANEDIOL × 4 CA CALCIUM ION × 2 GOL GLYCEROL × 1 TMP THYMIDINE-5'-PHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277.15 K；20 mM bicine pH7.5 300 mM Na-K tartrate 17.5% PEG 20K 10 mM praseodyme acetate
Resolution 2.00 Å R-free 0.252
9G9L DNA-PK + Polymerase lambda Deposited 2024-07-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 5 PDB declaration: heptameric
Chain F 1–575（575 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
9NPU Pre-catalytic ternary complex of DNA Polymerase Lambda with bound 1-nt gapped SSB substrate containing template ribonucleotide opposite primer terminus, and incoming dUMPNPP Deposited 2025-03-11 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 234–575（342 aa）
Not recorded SO4 SULFATE ION × 2 GOL GLYCEROL × 1 DUP 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；294 K；68 mM Na cacodylate pH 6.5, 20.4% (w/v) PEG8000, 136 mM ammonium sulfate, 12% (v/v) glycerol
Resolution 1.63 Å R-free 0.199

95 other PDB entries and 142 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DPOLL_HUMAN
Isoform —
PDB entities 9
Chains and sequence ranges Author chain A； PDBConstruct 1–575； UniProt 1–575

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 9gd7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9gd7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9gd7
Deposition date deposition_date2024-08-05
Structure title titleDNA-PK Ku80 mediated dimer bound to DNA polymerase Lambda and DNA ligase 4/XRCC4
Keywords keywordsKinase, complex, DNA-binding, 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_guinier67.07 Å
Radius of gyration Rg (electron density) rg_electron67.06 Å
Forward intensity I(0) i04819480000.00
Molecular weight molecular_weight593990.0 kDa
Excluded volume excluded_volume746460 ų
Envelope volume envelope_volume1170200 ų
Hydration-shell volume shell_volume145790 ų
Envelope diameter envelope_diameter230.3 Å
Shell Rg shell_rg67.39 Å
Envelope Rg envelope_rg65.59 Å
Shape Rg shape_rg67.08 Å
Total Rg total_rg67.00 Å
Total atoms total_atoms41717
Residues n_residues5208
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 dmax239.6 Å
Rg (real space) rg_real67.08 Å
Rg uncertainty (real space) rg_real_error2.26 Å
I(0) (real space) i0_real4.8200e+09
I(0) uncertainty (real space) i0_real_error1.0020e+08
Rg (reciprocal space) rg_reciprocal67.01 Å
I(0) (reciprocal space) i0_reciprocal4819000000.0000
Solution quality estimate total_estimate0.8589
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary72.9 Å
Skewness Skewness skewness0.325
Kurtosis Kurtosis kurtosis-0.378
Angular range angular_range— – 0.1150 Å−1
Current regularization parameter α current_alpha0.0018
Highest regularization parameter α highest_alpha449400000.0000
Real-space data points n_real_points24
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.788; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.798
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

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8. Citations (1)

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9. Files and Curves (10)