Two interaction surfaces between XPA and RPA organize the preincision complex in nucleotide excision repair

Kim M, Kim H, D’Souza A, Gallagher K, Jeong E, Topolska-Wós A, Ogorodnik Le Meur K, Tsai C, Tsai M, Kee M, Tainer J, Yeo J, Chazin W, Schärer O, Proceedings of the National Academy of Sciences 119(34) (2022) DOI

SASDPZ3 – Complex of XPA1-239 and RPAΔ32NΔ70N complex engaged on 3’ss-ds DNA junction NER substrate

DNA repair protein complementing XP-A cells
Replication protein A 70 kDa DNA-binding subunit
Replication protein A 32 kDa subunit
Replication protein A 14 kDa subunit
3-prime ss-ds DNA junction NER model substrate
MWI(0) 131 kDa
MWexpected 132 kDa
VPorod 189 nm3
log I(s) 6.03×101 6.03×100 6.03×10-1 6.03×10-2
DNA repair protein complementing XP-A cells Replication protein A 70 kDa DNA-binding subunit Replication protein A 32 kDa subunit Replication protein A 14 kDa subunit 3-prime ss-ds DNA junction NER model substrate small angle scattering data  s, nm-1
ln I(s)
DNA repair protein complementing XP-A cells Replication protein A 70 kDa DNA-binding subunit Replication protein A 32 kDa subunit Replication protein A 14 kDa subunit 3-prime ss-ds DNA junction NER model substrate Guinier plot ln 6.04×101 Rg: 4.3 nm 0 (4.3 nm)-2 s2
(sRg)2I(s)/I(0)
DNA repair protein complementing XP-A cells Replication protein A 70 kDa DNA-binding subunit Replication protein A 32 kDa subunit Replication protein A 14 kDa subunit 3-prime ss-ds DNA junction NER model substrate Kratky plot 1.104 0 3 sRg
p(r)
DNA repair protein complementing XP-A cells Replication protein A 70 kDa DNA-binding subunit Replication protein A 32 kDa subunit Replication protein A 14 kDa subunit 3-prime ss-ds DNA junction NER model substrate pair distance distribution function Rg: 4.3 nm 0 Dmax: 14.7 nm

Data validation


Fits and models


log I(s)
 s, nm-1
DNA repair protein complementing XP-A cells Replication protein A 70 kDa DNA-binding subunit Replication protein A 32 kDa subunit Replication protein A 14 kDa subunit 3-prime ss-ds DNA junction NER model substrate MES-FOXS model

Synchrotron SAXS data from solutions of 3' Complex of XPA and RPA in 20 mM Tris, 150 mM NaCl, 2% glycerol, 1 mM DTT, pH 8.0 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 50.00 μl sample was injected at a 0.50 ml/min flow rate onto a Shodex LW-803 column at 20°C. Data measured from solute-free fractions and the sample-elution peak were normalized to the intensity of the transmitted beam and radially averaged. The scattering of the solvent-blank was subtracted from the sample peak data produce the data displayed in this entry.

DNA repair protein complementing XP-A cells (XPA)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   27.3 kDa
 
UniProt   P23025 (1-239)
Sequence   FASTA
 
Replication protein A 70 kDa DNA-binding subunit (RPA70)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   49.2 kDa
 
UniProt   P27694 (185-616)
Sequence   FASTA
 
Replication protein A 32 kDa subunit (RPA32)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   24.9 kDa
 
UniProt   P15927 (45-270)
Sequence   FASTA
 
Replication protein A 14 kDa subunit (RPA14)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   13.6 kDa
 
UniProt   P35244 (1-121)
Sequence   FASTA
 
3-prime ss-ds DNA junction NER model substrate (3-prime DNA)
Mol. type   DNA
Olig. state   Monomer
Mon. MW   17.0 kDa
Sequence   FASTA