8RQC: CRBN-midi

Crystal structure of CRBN-midi in complex with mezigdomide and IKZF1 ZF2. Determined by X-ray diffraction at 2.15 Å resolution. Released 25 Sept 2024.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,303
Mol. weight: 84.39 kDa
Ligands: QFC, ZN
Released: 25 Sept 2024

Explore 8RQC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RQC contains 21 α-helices and 42 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	65-66	2	1
α-helix	73-74	2
β-strand	78-83	6	1
β-strand	96-101	6	1
α-helix	104-115	12
β-strand	119-123	5	1
β-strand	135-149	15	1
β-strand	152-172	21	1
β-strand	178-184	7	1
α-helix	185-186	2
β-strand	188	1	2
α-helix	251-265	15
α-helix	270-272	3
α-helix	277-286	10
α-helix	292-297	6
β-strand	303	1	2
α-helix	304-315	12
β-strand	320-323	4	3
β-strand	330-333	4	3
α-helix	334-336	3
β-strand	337	1	4
β-strand	346-350	5	4
β-strand	356-362	7	4
β-strand	368-370	3	4
β-strand	375	1	4
β-strand	384-391	8	4
β-strand	397-404	8	4
β-strand	413-418	6	4
α-helix	419-421	3
β-strand	422-424	3	3

Chain B: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	157-167	11

Chain D: 9 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	65-66	2	5
α-helix	71-74	4
β-strand	78-83	6	5
β-strand	96-101	6	5
α-helix	104-114	11
β-strand	119-125	7	5
β-strand	133-149	17	5
β-strand	152-172	21	5
β-strand	178-184	7	5
α-helix	185-186	2
β-strand	188	1	6
α-helix	251-262	12
α-helix	277-286	10
α-helix	292-299	8
β-strand	303	1	6
α-helix	304-315	12
β-strand	320-323	4	7
β-strand	330-333	4	7
α-helix	334-336	3
β-strand	337	1	8
β-strand	346-350	5	8
β-strand	356-362	7	8
β-strand	368-370	3	8
β-strand	375	1	8
β-strand	384-391	8	8
β-strand	397-404	8	8
β-strand	413-418	6	8
α-helix	419-421	3
β-strand	422-424	3	7

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	145-146	2	9
β-strand	153-154	2	9
α-helix	157-167	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein cereblon	A, D	protein	329	Homo sapiens	Q96SW2 (AlphaFold model)
DNA-binding protein Ikaros	B, E	protein	36	Homo sapiens	Q13422 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8RQC_1 Protein cereblon (chains A, D)
SAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSIQVIPVLPQVMMILVPGQTLPL
QLFHPQEVSMVRNLIQNDRTFAVLAYSNVQEREAEFGTTAEIYAYREEQDFGIEIVKVKA
IGRQRFKVLELRTQSDGIQQAKVQILPEGSGDAETLMDRIKKQLREWDENLKDDSLPSNP
IDFSYWVAANLPIDDSLRIQLLKIDSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEI
FSLSREGPMAAYVNPHGYVHEILTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASH
IGWKFTATKKDMSPQKFWGLTRSALIPTI

Sequence of entity 2 (B, E), FASTA

>8RQC_2 DNA-binding protein Ikaros (chains B, E)
GPGERPFQCNQCGASFTQKGNLLRHIKLHSGEKPFK

Ligands and cofactors

ID	Name	Formula	Copies
QFC	Mezigdomide	C32 H30 F N5 O4	2
ZN	Zinc ion	Zn	4

Primary citation

Design of a Cereblon construct for crystallographic and biophysical studies of protein degraders. Kroupova, A., Spiteri, V.A., Rutter, Z.J. et al. Nat Commun (2024) 15:8885-8885. DOI 10.1038/s41467-024-52871-9 · PubMed

Other PDB entries of the same protein (UniProt Q96SW2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4M91 1.1 Å, crystal structure of hN33/Tusc3-peptide 1
9CUO 1.6 Å, Crystal structure of CRBN with compound 3
9OHQ 1.6 Å, Structure of CRBN:IKZF2:Compound 15
9DOM 1.69 Å, PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of…
7BQV 1.8 Å, Cereblon in complex with SALL4 and (S)-5-hydroxythalidomide
9O91 1.86 Å, Structure of IKZF2:CRBN:Compound 5 ternary structure
7BQU 1.9 Å, Cereblon in complex with SALL4 and (S)-thalidomide
9GAO 1.95 Å, Crystal structure of CRBNmidi in complex with 2-(4-(2,6-dioxopiperidin-3-yl)phenoxy)-N-me…
9FJX 2.0 Å, Crystal structure of human CRBN-DDB1 in complex with Lenalidomide
8RQ8 2.19 Å, Crystal structure of CRBN-midi in complex with mezigdomide
9OHR 2.34 Å, Structure of CRBN:IKZF2:Compound 35
9SFM 2.39 Å, Crystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide

Browse structure collections

About this viewer

MolViewer shows 8RQC directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.