› 6q0v

X-ray diffraction
2.9Å resolution

Structure of DDB1-DDA1-DCAF15 complex bound to tasisulam and RBM39

Released:
DOI: 10.2210/pdb6q0v/pdb
PDB entry 6q0v coloured by chain, front view.
PDB entry 6q0v coloured by chain, side view.
PDB entry 6q0v coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural complementarity facilitates E7820-mediated degradation of RBM39 by DCAF15.
Faust TB, Yoon H, Nowak RP, Donovan KA, Li Z, Cai Q, Eleuteri NA, Zhang T, Gray NS, Fischer ES
OpenAccess logo Nat Chem Biol 16 7-14 (2020)
PMID: 31686031

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-172015 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
DNA damage-binding protein 1 Chain: A
Molecule details ›
Chain: A
Length: 864 amino acids
Theoretical weight: 96.43 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q16531 (Residues: 1-395, 706-1140; Coverage: 73%)
  • Best match: Q16531-2 (Residues: 59-451)
Gene names: DDB1, XAP1
Sequence domains:
DDB1- and CUL4-associated factor 15 Chain: B
Molecule details ›
Chain: B
Length: 276 amino acids
Theoretical weight: 31.61 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q66K64 (Residues: 34-260; Coverage: 38%)
Gene names: C19orf72, DCAF15
Sequence domains: DDB1-and CUL4-substrate receptor 15, WD repeat
DDB1- and CUL4-associated factor 15 Chain: C
Molecule details ›
Chain: C
Length: 263 amino acids
Theoretical weight: 29.89 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q66K64 (Residues: 383-600; Coverage: 36%)
Gene names: C19orf72, DCAF15
RNA-binding protein 39 Chain: D
Molecule details ›
Chain: D
Length: 107 amino acids
Theoretical weight: 12.06 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q14498 (Residues: 250-332; Coverage: 16%)
Gene names: HCC1, RBM39, RNPC2
Sequence domains: RNA recognition motif
DET1- and DDB1-associated protein 1 Chain: E
Molecule details ›
Chain: E
Length: 126 amino acids
Theoretical weight: 14.54 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9BW61 (Residues: 1-102; Coverage: 100%)
Gene names: C19orf58, DDA1, PCIA1
Sequence domains: Det1 complexing ubiquitin ligase

Ligands and Environments

2 bound ligands:
Ligand P7M 1 x P7M
Ligand ZN 1 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 81.769Å b: 94.613Å c: 260.39Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.206 0.242
Expression system: Trichoplusia ni

Quick links

Citations

30 review citations

PROTAC targeted protein degraders: the past is prologue.
Békés et al. (2022)
29 more

2 mentions without citation

Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction.
Rui et al. (2023)
1 more