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

SASDFF5 – Protein DPCD

Protein DPCD
MWexperimental 23 kDa
MWexpected 24 kDa
VPorod 39 nm3
log I(s) 2.20×10-2 2.20×10-3 2.20×10-4 2.20×10-5
Protein DPCD small angle scattering data  s, nm-1
ln I(s)
Protein DPCD Guinier plot ln 2.20×10-2 Rg: 2.2 nm 0 (2.2 nm)-2 s2
(sRg)2I(s)/I(0)
Protein DPCD Kratky plot 1.104 0 3 sRg
p(r)
Protein DPCD pair distance distribution function Rg: 2.4 nm 0 Dmax: 12.3 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Protein DPCD DAMMIF model

log I(s)
 s, nm-1
Protein DPCD ROSETTA model

log I(s)
 s, nm-1
Protein DPCD SREFLEX model

log I(s)
 s, nm-1
Protein DPCD GASBOR model

Synchrotron SAXS data from solutions of Protein DPCD 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: 12 mg/mL; Injection volume: 50 μL. The data were collected through the SEC peak of the protein as a series of 33 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 the volume of correlation, Vc.

Protein DPCD
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   23.5 kDa
 
UniProt   Q9BVM2
Sequence   FASTA