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) Europe PMC

SASDJX4 – DNA-dependent protein kinase catalytic subunit (DNA-PKcs)

DNA-dependent protein kinase catalytic subunit

MW^experimental	480	kDa
MW^expected	468	kDa
V^Porod	1040	nm³

log I(s) 4.77×10³ 4.77×10² 4.77×10¹ 4.77×10⁰

DNA-dependent protein kinase catalytic subunit small angle scattering data

s, nm^-1

Log plot Log-Log plot

ln I(s)

DNA-dependent protein kinase catalytic subunit Guinier plot

ln 4.78×10³ R_g: 5.6 nm 0 (5.6 nm)^-2 s²

(sR_g)²I(s)/I(0)

DNA-dependent protein kinase catalytic subunit Kratky plot

1.104 0 √3 sR_g

p(r)	R_g: 5.4 nm 0 D_max: 15.6 nm

Data validation

Fits and models

log I(s)	s, nm^-1
+3 Δ/σ -3	s, nm^-1

DNA-dependent protein kinase catalytic subunit BILBOMD model

Synchrotron SAXS data from solutions of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) in 50 mM Tris-HCl, 100 mM NaCl, 5% glycerol, 0.01% sodium azide, pH 7.5 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS) storage ring (Berkeley, CA, USA) using a MAR 165 CCD detector at a sample-detector distance of 1.5 m and at a wavelength of λ = 0.103 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50.00 μl sample at 10 mg/ml was injected at a 0.25 ml/min flow rate onto a Shodex KW403-4F column at 20°C. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Storage temperature = UNKNOWN. Number of frames = UNKNOWN

DNA-dependent protein kinase catalytic subunit (DNA-PKcs)
Mol. type		Protein
Organism		Homo sapiens
Olig. state		Monomer
Mon. MW		468.3 kDa

UniProt		P78527 (10-4128)
Sequence		FASTA