› 6sj7

Electron Microscopy
3.54Å resolution

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

Released:
DOI: 10.2210/pdb6sj7/pdb
PDB entry 6sj7 coloured by chain, front view.
PDB entry 6sj7 coloured by chain, side view.
PDB entry 6sj7 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of indisulam-mediated RBM39 recruitment to DCAF15 E3 ligase complex.
Bussiere DE, Xie L, Srinivas H, Shu W, Burke A, Be C, Zhao J, Godbole A, King D, Karki RG, Hornak V, Xu F, Cobb J, Carte N, Frank AO, Frommlet A, Graff P, Knapp M, Fazal A, Okram B, Jiang S, Michellys PY, Beckwith R, Voshol H, Wiesmann C, Solomon JM, Paulk J
Nat Chem Biol 16 15-23 (2020)
PMID: 31819272
Related structures: EMD-10213

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-172016 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
DDB1- and CUL4-associated factor 15 Chain: A
Molecule details ›
Chain: A
Length: 601 amino acids
Theoretical weight: 66.56 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q66K64 (Residues: 1-600; Coverage: 100%)
Gene names: C19orf72, DCAF15
Sequence domains: DDB1-and CUL4-substrate receptor 15, WD repeat
DNA damage-binding protein 1 Chain: B
Molecule details ›
Chain: B
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:
RNA-binding protein 39 Chain: C
Molecule details ›
Chain: C
Length: 81 amino acids
Theoretical weight: 9.09 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q14498 (Residues: 248-328; Coverage: 15%)
Gene names: HCC1, RBM39, RNPC2
Sequence domains: RNA recognition motif
DET1- and DDB1-associated protein 1 Chain: D
Molecule details ›
Chain: D
Length: 101 amino acids
Theoretical weight: 11.72 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9BW61 (Residues: 2-102; Coverage: 99%)
Gene names: C19orf58, DDA1, PCIA1
Sequence domains: Det1 complexing ubiquitin ligase

Ligands and Environments

1 bound ligand:
Ligand EF6 1 x EF6
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.54Å
Relevant EMDB volumes: EMD-10213
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli BL21(DE3)

Quick links

Citations

39 review citations

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

3 mentions without citation

Applications and prospects of cryo-EM in drug discovery.
Zhu et al. (2023)
2 more