Deciphering cellular and molecular determinants of human DPCD protein in complex with RUVBL1/RUVBL2 AAA-ATPases.

Dos Santos Morais R, Santo PE, Ley M, Schelcher C, Abel Y, Plassart L, Deslignière E, Chagot ME, Quinternet M, Paiva ACF, Hessmann S, Morellet N, M F Sousa P, Vandermoere F, Bertrand E, Charpentier B, Bandeiras TM, Plisson-Chastang C, Verheggen C, Cianférani S, Manival X, J Mol Biol :167760 (2022) Europe PMC

SASDFH5 – DPCD His-RuvBl1/RuvBl2 hexamer complex

Protein DPCD
RuvB-like 1
RuvB-like 2
MWexperimental 370 kDa
MWexpected 381 kDa
VPorod 856 nm3
log I(s) 9.06×10-2 9.06×10-3 9.06×10-4 9.06×10-5
Protein DPCD RuvB-like 1 RuvB-like 2 small angle scattering data  s, nm-1
ln I(s)
Protein DPCD RuvB-like 1 RuvB-like 2 Guinier plot ln 9.07×10-2 Rg: 5.4 nm 0 (5.4 nm)-2 s2
(sRg)2I(s)/I(0)
Protein DPCD RuvB-like 1 RuvB-like 2 Kratky plot 1.104 0 √3 sRg
p(r)
Protein DPCD RuvB-like 1 RuvB-like 2 pair distance distribution function Rg: 5.3 nm 0 Dmax: 15.9 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Protein DPCD RuvB-like 1 RuvB-like 2 GASBOR model
log I(s)
 s, nm-1
Protein DPCD RuvB-like 1 RuvB-like 2 DAMMIF model
Synchrotron SAXS data from solutions of the DPCD His-RuvBl1/RuvBl2 hexamer complex in 20 mM HEPES, 150 mM NaCl, 1% glycerol, 5 mM TCEP, pH 7.5 were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the SWING beam line at SOLEIL (Saint-Aubin, France) using a Eiger 4M detector at a sample-detector distance of 2 m and at a wavelength of λ = 0.1033 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 15°C using the following parameters: Column: BioSEC5-500A (4.6 mm id * 300 mm); Flow rate: 0.3 mL/min; Sample injection concentration: 4 mg/mL; Injection volume: 50 μL. The data were collected through the SEC peak of the protein as a series of 41 x 1 second exposures. Each unsubtracted data frame was normalised to the intensity of the transmitted beam and radially averaged and the scattering of an appropriate solvent-blank was subtracted. The resulting subtracted frames were scaled and averaged to generate the final SAXS profile displayed in this entry.

The experimental molecular weight was determined from SEC-RALS/LALS experiment (370 kDa).

Protein DPCD
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Trimer
Mon. MW   23.5 kDa
 
UniProt   Q9BVM2
Sequence   FASTA
 
RuvB-like 1
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Trimer
Mon. MW   51.8 kDa
 
UniProt   Q9Y265
Sequence   FASTA
 
RuvB-like 2
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Trimer
Mon. MW   51.9 kDa
 
UniProt   Q9Y230
Sequence   FASTA