Structure of a collagen VI α3 chain VWA domain array: adaptability and functional implications of myopathy causing mutations

Solomon-Degefa H, Gebauer J, Jeffries C, Freiburg C, Meckelburg P, Bird L, Baumann U, Svergun D, Owens R, Werner J, Behrmann E, Paulsson M, Wagener R, Journal of Biological Chemistry :jbc.RA120.014865 (2020) DOI

SASDEY9 – Collagen VI von Willebrand factor (VWA) double-domain fragment, N5N4

Collagen, type VI, alpha 3
MWexperimental 43 kDa
MWexpected 44 kDa
VPorod 66 nm3
log I(s) 2.86×102 2.86×101 2.86×100 2.86×10-1
Collagen, type VI, alpha 3 small angle scattering data  s, nm-1
ln I(s)
Collagen, type VI, alpha 3 Guinier plot ln 2.87×102 Rg: 2.9 nm 0 (2.9 nm)-2 s2
(sRg)2I(s)/I(0)
Collagen, type VI, alpha 3 Kratky plot 1.104 0 3 sRg
p(r)
Collagen, type VI, alpha 3 pair distance distribution function Rg: 2.9 nm 0 Dmax: 9.9 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Collagen VI von Willebrand factor (VWA) double-domain fragment, N5N4 Rg histogram Rg, nm

log I(s)
 s, nm-1
Collagen, type VI, alpha 3 DAMMIN model
Collagen, type VI, alpha 3 DAMFILT model

log I(s)
 s, nm-1
Collagen, type VI, alpha 3 GASBOR model

log I(s)
 s, nm-1
Collagen, type VI, alpha 3 BUNCH model

Synchrotron SAXS data from solutions of the collagen VI N5N4 double-domain fragment in 20 mM Tris, pH 7.4, 150mM NaCl 3% v/v glycerol, were collected using size-exclusion chromatography SAXS (SEC-SAXS) on the EMBL P12 beam line at PETRA III (DESY, Hamburg, Germany) equipped with a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). SEC-SAXS was performed at 20°C using the following parameters: Column: GE-Healthcare S75 Increase 10/300 analytical SEC column; Flow rate: 0.6 mL/min; Sample injection concentration: 12.0 mg/mL; Injection volume: 55 μL. Total X-ray acquisition time = 2400 s. The data were collected through the SEC peak of the protein as a series of 18 x 1 second exposures and processed using CHROMIXS (Panjkovich & Svergun, 2018 Bioinformatics 34(11):1944-1946) that was also used to select an appropriate matched solvent-blank. Parallel inline multi-angle laser and dynamic light scattering with refractive index measurements (SEC-MALLS/DLS/RI) were performed using a Wyatt Mini-Dawn TREOS with an in-built quasi elastic light scattering (QELS) module coupled to an OptiLab T-Rex refractometer. The quoted experiential MW for this entry is derived from MALLS. Concentration-independent MW estimates obtained directly from the SAXS data using DATMW (Hajizadeh et al., 2018 Scientific Reports 8, 7204), as part of CHROMIXS/ATSAS 2.8.3, as well as the SEC-MALLS/DLS/RI data and additional modelling files, including ITASSER homology modelling (Yang et al., 2015 Nature Methods 12, 7-8) are included in the full-entry zip archive.

Collagen, type VI, alpha 3 (N5N4)
Mol. type   Protein
Organism   Mus musculus
Olig. state   Monomer
Mon. MW   44.3 kDa
 
UniProt   D3YWD1 (1023-1425)
Sequence   FASTA
 
PDB code   4IGI