6pai

X-ray diffraction
2.9Å resolution

Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and sulfonamide E7820

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
Non-polymer only tetramer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
DNA damage-binding protein 1 Chain: A
Molecule details ›
Chain: A
Length: 1140 amino acids
Theoretical weight: 127.1 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q16531 (Residues: 1-1140; Coverage: 100%)
Gene names: DDB1, XAP1
Sequence domains:
DDB1- and CUL4-associated factor 15 Chain: C
Molecule details ›
Chain: C
Length: 498 amino acids
Theoretical weight: 56.41 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q66K64 (Residues: 2-600; Coverage: 82%)
Gene names: C19orf72, DCAF15
Sequence domains: DDB1-and CUL4-substrate receptor 15, WD repeat
RNA-binding protein 39 Chain: D
Molecule details ›
Chain: D
Length: 109 amino acids
Theoretical weight: 12.1 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q14498 (Residues: 235-331; Coverage: 18%)
Gene names: HCC1, RBM39, RNPC2
Sequence domains: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
DET1- and DDB1-associated protein 1 Chain: E
Molecule details ›
Chain: E
Length: 102 amino acids
Theoretical weight: 11.86 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
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:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: P21
Unit cell:
a: 81.507Å b: 94.767Å c: 145.706Å
α: 90° β: 98.06° γ: 90°
R-values:
R R work R free
0.21 0.208 0.252
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli