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 Oct 15)

doi: 10.1038/s41467-024-52871-9

Submitted to SASBDB: 2024 Jan 17 Published in SASBDB: 2024 Sep 27

SASDU52 – Cereblon-midi (CRBNmidi), an engineered Cereblon construct for crystallographic and biophysical studies, apo form Sample: Cereblon-midi monomer, 37 kDa protein Buffer: 20 mM Hepes, 500 mM NaCl, 0.5 mM TCEP, pH: 7.5 Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Mar 1 RgGuinier 2.7 nm Dmax 8.6 nm VolumePorod 61 nm3

SASDU62 – Cereblon-midi (CRBNmidi), an engineered Cereblon construct for crystallographic and biophysical studies, bound to Mezigdomide Sample: Cereblon-midi monomer, 37 kDa protein Mezigdomide monomer, 1 kDa synthetic construct Buffer: 20 mM Hepes, 500 mM NaCl, 0.5 mM TCEP, pH: 7.5 Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Mar 1 RgGuinier 2.3 nm Dmax 7.3 nm VolumePorod 60 nm3

SASDU72 – Cereblon-midi (CRBNmidi), an engineered Cereblon construct for crystallographic and biophysical studies, bound to Pomalidomide Sample: Cereblon-midi monomer, 37 kDa protein Pomalidomide monomer, 0 kDa synthetic construct Buffer: 20 mM Hepes, 500 mM NaCl, 0.5 mM TCEP, pH: 7.5 Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Mar 1 RgGuinier 2.3 nm Dmax 6.9 nm VolumePorod 63 nm3

SASDU82 – Cereblon-midi (CRBNmidi), an engineered Cereblon construct for crystallographic and biophysical studies, bound to Iberdomide Sample: Cereblon-midi monomer, 37 kDa protein Iberdomide monomer, 0 kDa synthetic construct Buffer: 20 mM Hepes, 500 mM NaCl, 0.5 mM TCEP, pH: 7.5 Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Mar 1 RgGuinier 2.4 nm Dmax 7.7 nm VolumePorod 68 nm3

SASDU92 – Cereblon-midi (CRBNmidi), an engineered Cereblon construct for crystallographic and biophysical studies, bound to Lenalidomide Sample: Cereblon-midi monomer, 37 kDa protein Lenalidomide monomer, 0 kDa synthetic construct Buffer: 20 mM Hepes, 500 mM NaCl, 0.5 mM TCEP, pH: 7.5 Experiment: SAXS data collected at B21, Diamond Light Source on 2023 Mar 1 RgGuinier 2.2 nm Dmax 6.2 nm VolumePorod 59 nm3