› 8u15

X-ray diffraction
2.95Å resolution

The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to CC-220

Released:
DOI: 10.2210/pdb8u15/pdb
PDB entry 8u15 coloured by chain, front view.
PDB entry 8u15 coloured by chain, side view.
PDB entry 8u15 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and biophysical comparisons of the pomalidomide- and CC-220-induced interactions of SALL4 with cereblon.
Ma X, Leon B, Ornelas E, Dovala D, Tandeske L, Luu C, Pardee G, Widger S, Solomon JM, Beckwith REJ, Moser H, Clifton MC, Wartchow CA
OpenAccess logo Sci Rep 13 22088 (2023)
PMID: 38086859

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-556905 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Protein cereblon Chains: A, D
Molecule details ›
Chains: A, D
Length: 373 amino acids
Theoretical weight: 42.97 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q96SW2 (Residues: 70-442; Coverage: 84%)
Gene names: AD-006, CRBN
Sequence domains:
DNA damage-binding protein 1 Chains: B, E
Molecule details ›
Chains: B, E
Length: 836 amino acids
Theoretical weight: 93.35 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q16531 (Residues: 1-1140; Coverage: 73%)
  • Best match: Q16531-2 (Residues: 59-451)
Gene names: DDB1, XAP1
Sequence domains:
Sal-like protein 4 Chains: C, F
Molecule details ›
Chains: C, F
Length: 55 amino acids
Theoretical weight: 6.42 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UJQ4 (Residues: 379-432; Coverage: 5%)
Gene names: SALL4, ZNF797
Sequence domains: Zinc finger, C2H2 type

Ligands and Environments

3 bound ligands:
Ligand ZN 6 x ZN
Ligand 8W7 2 x 8W7
Ligand SO4 12 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P21
Unit cell:
a: 110.729Å b: 95.727Å c: 150.947Å
α: 90° β: 91.72° γ: 90°
R-values:
R R work R free
0.222 0.22 0.272
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli

Quick links

Citations

1 citations in other articles

Development of sulfonyl fluoride chemical probes to advance the discovery of cereblon modulators.
Liu et al. (2024)

1 mention without citation

Structural and biophysical comparisons of the pomalidomide- and CC-220-induced interactions of SALL4 with cereblon.
Ma et al. (2023)