Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders

Kroupova A, Spiteri V, Rutter Z Furihata H, Darren D, Ramachandran S, Chakraborti S, Haubrich K, Pethe J, Gonzales D, Wijaya A, Rodriguez-Rios M, Sturbaut M, Lynch D, Farnaby W, Nakasone M, Zollman D, Ciulli A, Nature Communications 15(1) (2024) DOI

SASDVN6 – Cereblon-midi (CRBNmidi), an engineered Cereblon construct for crystallographic and biophysical studies, bound to Boc-VcN

Cereblon-midi
MWexperimental 37 kDa
MWexpected 37 kDa
VPorod 63 nm3
log I(s) 2.07×10-2 2.07×10-3 2.07×10-4 2.07×10-5
Cereblon-midi small angle scattering data  s, nm-1
ln I(s)
Cereblon-midi Guinier plot ln 2.07×10-2 Rg: 2.3 nm 0 (2.3 nm)-2 s2
(sRg)2I(s)/I(0)
Cereblon-midi Kratky plot 1.104 0 3 sRg
p(r)
Cereblon-midi pair distance distribution function Rg: 2.4 nm 0 Dmax: 9.1 nm

Data validation


There are no models related to this curve.

Synchrotron SAXS data from solutions of CRBNmidi bound to Boc-VcN in 20 mM HEPES, 500 mM NaCl, 0.5 mM TCEP, pH 7.5 were collected on the B21 beam line at the Diamond Light Source (Didcot, UK) using a Eiger 4M detector at a sample-detector distance of 3.7 m and at a wavelength of λ = 0.09464 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 3.4 mg/ml was injected at a 0.08 ml/min flow rate onto a Cytiva Superdex 200 Increase 3.2/300 column at 15°C. 600 successive 3 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.

CRBN-midi, an engineered Cereblon construct for crystallographic and biophysical studies of protein degraders (derived from human Cereblon, Uniprot Q96SW2).

Cereblon-midi (CRBNmidi)
Mol. type   Protein
Organism   synthetic construct
Olig. state   Monomer
Mon. MW   37.4 kDa
Sequence   FASTA