› 6q0r

X-ray diffraction
2.9Å resolution

Structure of DDB1-DDA1-DCAF15 complex bound to E7820 and RBM39

Released:
DOI: 10.2210/pdb6q0r/pdb
PDB entry 6q0r coloured by chain, front view.
PDB entry 6q0r coloured by chain, side view.
PDB entry 6q0r 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
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%)
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

3 bound ligands:
Ligand OXM 1 x OXM
Ligand O6M 1 x O6M
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: 81.108Å b: 93.6Å c: 258.439Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.207 0.205 0.251
Expression system: Trichoplusia ni

Quick links

Citations

28 review citations

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

7 mentions without citation

Targeted protein degradation as a powerful research tool in basic biology and drug target discovery.
Wu et al. (2020)
6 more