Flexibility and distributive synthesis regulate RNA priming and handoff in human DNA polymerase α-primase

Cordoba J, Mullins E, Salay L, Eichman B, Chazin W, Journal of Molecular Biology :168330 (2023) DOI

SASDS87 – polymerase alpha-primase polΔcat-prim in the absence of substrate

DNA polymerase alpha subunit B
DNA polymerase alpha catalytic subunit
DNA primase large subunit
DNA primase small subunit
MWexperimental 180 kDa
MWexpected 181 kDa
VPorod 300 nm3
log I(s) 6.41×102 6.41×101 6.41×100 6.41×10-1
DNA polymerase alpha subunit B DNA polymerase alpha catalytic subunit DNA primase large subunit DNA primase small subunit small angle scattering data  s, nm-1
ln I(s)
DNA polymerase alpha subunit B DNA polymerase alpha catalytic subunit DNA primase large subunit DNA primase small subunit Guinier plot ln 6.42×102 Rg: 4.6 nm 0 (4.6 nm)-2 s2
(sRg)2I(s)/I(0)
DNA polymerase alpha subunit B DNA polymerase alpha catalytic subunit DNA primase large subunit DNA primase small subunit Kratky plot 1.104 0 3 sRg
p(r)
DNA polymerase alpha subunit B DNA polymerase alpha catalytic subunit DNA primase large subunit DNA primase small subunit pair distance distribution function Rg: 4.7 nm 0 Dmax: 15.1 nm

Data validation


Fits and models


log I(s)
 s, nm-1
DNA polymerase alpha subunit B DNA polymerase alpha catalytic subunit DNA primase large subunit DNA primase small subunit BILBOMD model

Synchrotron SAXS data from solutions of polΔcat-prim in the absence of substrate in 20 mM HEPES, 150 mM NaCl, 5 mM MgCl2, 1 mM TCEP, pH 7.5 were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS; Berkeley, CA, USA) using a Pilatus3 X 2M 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 60.00 μl sample at 5 mg/ml was injected at a 0.65 ml/min flow rate onto a Shodex LW-803 column at 23°C. 500 successive 3 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

DNA polymerase alpha subunit B
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   49.2 kDa
 
UniProt   Q14181 (155-598)
Sequence   FASTA
 
DNA polymerase alpha catalytic subunit
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   23.1 kDa
 
UniProt   P09884 (1265-1462)
Sequence   FASTA
 
DNA primase large subunit
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   58.8 kDa
 
UniProt   P49643 (1-509)
Sequence   FASTA
 
DNA primase small subunit
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   50.0 kDa
 
UniProt   P49642 (1-420)
Sequence   FASTA