The vaccinia virus DNA polymerase structure provides insights into the mode of processivity factor binding

Tarbouriech N, Ducournau C, Hutin S, Mas P, Man P, Forest E, Hart D, Peyrefitte C, Burmeister W, Iseni F, Nature Communications 2017 Dec 8(1) DOI

SASDCM5 – Vaccinia virus binary E9 polymerase / DNA complex

DNA polymerase E9 exo- mutant
DNA oligomer template-primer hairpin
MWexperimental 127 kDa
MWexpected 126 kDa
VPorod 210 nm3
log I(s) 8.79×101 8.79×100 8.79×10-1 8.79×10-2
DNA polymerase E9 exo- mutant DNA oligomer template-primer hairpin small angle scattering data  s, nm-1
ln I(s)
DNA polymerase E9 exo- mutant DNA oligomer template-primer hairpin Guinier plot ln 8.79×101 Rg: 3.5 nm 0 (3.5 nm)-2 s2
(sRg)2I(s)/I(0)
DNA polymerase E9 exo- mutant DNA oligomer template-primer hairpin Kratky plot 1.104 0 3 sRg
p(r)
DNA polymerase E9 exo- mutant DNA oligomer template-primer hairpin pair distance distribution function Rg: 3.5 nm 0 Dmax: 12 nm

Experimental data validation


Fits and models


log I(s)
 s, nm-1
DNA polymerase E9 exo- mutant DNA oligomer template-primer hairpin PYMOL model
Synchrotron SAXS data from solutions of Binary E9 polymerase / DNA complex in 20 mM Tris HCl, 100 mM NaCl, 4 mM DTT, pH 7 were collected using size exclusion chromatography coupled SAXS (SEC-SAXS) on the BM29 beam line at the ESRF (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.0992 nm (I(s) vs s, where s = 4πsinθ/λ and 2θ is the scattering angle). Data were collected at at 20°C during the course of elution (700 successive 1 second frames). The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted and the resulting subtracted curves were scaled and averaged.

DNA polymerase E9 exo- mutant (E9 exo-)
Mol. type   Protein
Organism   Vaccinia virus (strain Copenhagen)
Olig. state   Monomer
Mon. MW   117.1 kDa
 
UniProt   P20509 (1-1006)
Sequence   FASTA
 
DNA oligomer template-primer hairpin (DNA hairpin)
Mol. type   DNA
Organism   synthetic construct
Olig. state   Monomer
Mon. MW   9.0 kDa
Sequence   FASTA
 
PDB code   5N2H