MPBuilder: A PyMOL Plugin for Building and Refinement of Solubilized Membrane Proteins Against Small Angle X-ray Scattering Data

Molodenskiy D, Svergun D, Mertens H, Journal of Molecular Biology :166888 (2021) DOI

SASDKK4 – A-type ATP synthase

n-Dodecyl-β-D-Maltopyranoside
A-type ATP synthase
Monoclonal Antibody Fragment
MWexperimental 814 kDa
MWexpected 765 kDa
VPorod 1549 nm3
log I(s) 1.17×10-1 1.17×10-2 1.17×10-3 1.17×10-4
n-Dodecyl-β-D-Maltopyranoside A-type ATP synthase Monoclonal Antibody Fragment small angle scattering data  s, nm-1
ln I(s)
n-Dodecyl-β-D-Maltopyranoside A-type ATP synthase Monoclonal Antibody Fragment Guinier plot ln 1.17×10-1 Rg: 8.0 nm 0 (8.0 nm)-2 s2
(sRg)2I(s)/I(0)
n-Dodecyl-β-D-Maltopyranoside A-type ATP synthase Monoclonal Antibody Fragment Kratky plot 1.104 0 √3 sRg
p(r)
n-Dodecyl-β-D-Maltopyranoside A-type ATP synthase Monoclonal Antibody Fragment pair distance distribution function Rg: 8.3 nm 0 Dmax: 27 nm

Data validation

Fits and models

log I(s)
 s, nm-1
n-Dodecyl-β-D-Maltopyranoside A-type ATP synthase Monoclonal Antibody Fragment OTHER model
Synchrotron SAXS data from solutions of A-type ATP synthase in 20 mM Tris/HCl, 100 mM sucrose, 100 mM NaCl, 2 mM MgCl2, 10% glycerol, 0.05% b-DDM, pH 8 were collected on the SAXS/WAXS beam line at the Australian Synchrotron storage ring (Melbourne, Australia) using a Pilatus 1M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.113 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 at 10 mg/ml was injected at a 0.50 ml/min flow rate onto a Wyatt WTC-030S5 5μm 300+, 7.8x300 mm column at 20°C. 2400 successive 1 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.

n-Dodecyl-β-D-Maltopyranoside (b-DDM)
Mol. type   Other
Organism   synthetic construct
Olig. state   Other
Mon. MW   0.5 kDa
A-type ATP synthase (AATP synthase)
Mol. type   Protein
Organism   Thermus thermophilus
Olig. state   Monomer
Mon. MW   655.0 kDa
Sequence   FASTA
 
Monoclonal Antibody Fragment (monoclonal antibody)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Dimer
Mon. MW   16.3 kDa
Sequence   FASTA
 
PDB ID   6R10