Visualizing functional dynamicity in the DNA-dependent protein kinase holoenzyme DNA-PK complex by integrating SAXS with cryo-EM.

Hammel M, Rosenberg DJ, Bierma J, Hura GL, Lees-Miller SP, Tainer JA
Prog Biophys Mol Biol (2020 Sep 20)

PMID: 32966823 doi: 10.1016/j.pbiomolbio.2020.09.003

Submitted to SASBDB: 2020 Jun 23 Published in SASBDB: 2020 Jul 16

SASDJV4 – X-ray repair cross-complementing proteins 5ΔCTR and 6 Sample: X-ray repair cross-complementing protein 6 monomer, 70 kDa Homo sapiens protein X-ray repair cross-complementing protein 5 ΔCTR monomer, 64 kDa Homo sapiens protein Buffer: 50 mM Hepes, 50 mM KCl, 5 mM MgCl2, 5% glycerol and 0.2 mM DTT, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Mar 12 RgGuinier 3.8 nm Dmax 12.5 nm VolumePorod 240 nm3

SASDJU4 – X-ray repair cross-complementing proteins 5 and 6 Sample: X-ray repair cross-complementing protein 6 monomer, 70 kDa Homo sapiens protein X-ray repair cross-complementing protein 5 monomer, 83 kDa Homo sapiens protein Buffer: 50 mM Hepes, 50 mM KCl, 5 mM MgCl2, 5% glycerol and 0.2 mM DTT, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2019 Mar 12 RgGuinier 4.2 nm Dmax 14.9 nm VolumePorod 253 nm3

SASDJW4 – X-ray repair cross-complementing proteins 5 and 6-DNA Sample: X-ray repair cross-complementing protein 6 monomer, 70 kDa Homo sapiens protein X-ray repair cross-complementing protein 5 monomer, 83 kDa Homo sapiens protein Y-DNA monomer, 18 kDa DNA Buffer: 50 mM Tris-HCl, 100 mM NaCl, 5% glycerol, 0.01% sodium azide, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2010 Jan 8 RgGuinier 4.1 nm Dmax 14.8 nm VolumePorod 280 nm3

SASDJX4 – DNA-dependent protein kinase catalytic subunit (DNA-PKcs) Sample: DNA-dependent protein kinase catalytic subunit monomer, 468 kDa Homo sapiens protein Buffer: 50 mM Tris-HCl, 100 mM NaCl, 5% glycerol, 0.01% sodium azide, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Dec 30 RgGuinier 5.6 nm Dmax 15.6 nm VolumePorod 1040 nm3

SASDJY4 – Autophosphorylated DNA-dependent protein kinase (DNA-PKcs) Sample: DNA-dependent protein kinase catalytic subunit monomer, 468 kDa Homo sapiens protein Buffer: 50 mM Tris-HCl, 100 mM KCl, 5% (v/v) glycerol, 0.2 mM EDTA containing 0.1 mM benzamidine, 0.2 mM PMSF and 0.2 µg/ml pepstatin, pH: 8 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2010 Jan 8 RgGuinier 5.5 nm Dmax 16.1 nm VolumePorod 918 nm3

SASDJZ4 – DNA-dependent protein kinase/ X-ray repair cross-complementing protein 5 and 6 complex bound to DNA (DNA-PK monomer ) Sample: X-ray repair cross-complementing protein 6 monomer, 70 kDa Homo sapiens protein X-ray repair cross-complementing protein 5 monomer, 83 kDa Homo sapiens protein DNA-dependent protein kinase catalytic subunit monomer, 468 kDa Homo sapiens protein DsDNA dimer, 21 kDa DNA Buffer: 50 mM Tris-HCl, 100 mM NaCl, 5% glycerol, 0.01% sodium azide, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Dec 30 RgGuinier 6.5 nm Dmax 23.1 nm VolumePorod 1090 nm3

SASDJ25 – DNA-dependent protein kinase/ X-ray repair cross-complementing protein 5 and 6 complex bound to DNA (DNA-PK monomer/dimer) Sample: X-ray repair cross-complementing protein 6 monomer, 70 kDa Homo sapiens protein X-ray repair cross-complementing protein 5 monomer, 83 kDa Homo sapiens protein DNA-dependent protein kinase catalytic subunit monomer, 468 kDa Homo sapiens protein DsDNA dimer, 21 kDa DNA Buffer: 50 mM Tris-HCl, 100 mM NaCl, 5% glycerol, 0.01% sodium azide, pH: 7.5 Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2016 Dec 30 RgGuinier 7.5 nm Dmax 29.4 nm VolumePorod 1440 nm3