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

SASDJJ4 – Collagen VI von Willebrand factor (VWA) N2 domain

Collagen alpha-3(VI) chain, N2 domain
MWexperimental 22 kDa
MWexpected 22 kDa
VPorod 40 nm3
log I(s) 1.13×102 1.13×101 1.13×100 1.13×10-1
Collagen alpha-3(VI) chain, N2 domain small angle scattering data  s, nm-1
ln I(s)
Collagen alpha-3(VI) chain, N2 domain Guinier plot ln 1.13×102 Rg: 1.8 nm 0 (1.8 nm)-2 s2
(sRg)2I(s)/I(0)
Collagen alpha-3(VI) chain, N2 domain Kratky plot 1.104 0 √3 sRg
p(r)
Collagen alpha-3(VI) chain, N2 domain pair distance distribution function Rg: 1.8 nm 0 Dmax: 5.8 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Collagen alpha-3(VI) chain, N2 domain DAMMIN model
Collagen alpha-3(VI) chain, N2 domain DAMFILT model
log I(s)
 s, nm-1
Collagen alpha-3(VI) chain, N2 domain GASBOR model
log I(s)
 s, nm-1
Collagen alpha-3(VI) chain, N2 domain ITASSER model
Synchrotron SAXS data from solutions of the N2 domain from Collagen VI in 20 mM TRIS, pH 7.4, 150mM NaCl 3% v/v glycerol, were collected on the EMBL P12 beam line at PETRA III (DESY, Hamburg, Germany) using a Pilatus 6M detector at a sample-detector distance of 3 m and at a wavelength of λ = 0.124 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 25.00 μl sample at 20 mg/ml was injected at a 0.60 ml/min flow rate onto a GE Superdex 75 Increase 10/300 column at 20°C. 39 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.

Additional SEC-SAXS and SEC-MALLS information are provided in the full entry zip archive.

Collagen alpha-3(VI) chain, N2 domain (N2 domain)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   22.1 kDa
 
UniProt   P12111 (1634-1833)
Sequence   FASTA