PDBe 5d2m

X-ray diffraction
2.4Å resolution

Complex between human SUMO2-RANGAP1, UBC9 and ZNF451

Released:
Source organism: Homo sapiens
Primary publication:
Structural basis for catalytic activation by the human ZNF451 SUMO E3 ligase.
OpenAccess logo Nat. Struct. Mol. Biol. (2015)
PMID: 26524494

Function and Biology Details

Structure analysis Details

Assemblies composition:
hetero pentamer (preferred)
hetero dimer
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
SUMO-conjugating enzyme UBC9 Chains: A, D
Molecule details ›
Chains: A, D
Length: 161 amino acids
Theoretical weight: 18.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: NEW P63279 (Residues: 1-158; Coverage: 100%)
Gene names: UBC9, UBCE9, UBE2I
Sequence domains: Ubiquitin-conjugating enzyme
Structure domains: Ubiquitin Conjugating Enzyme
Small ubiquitin-related modifier 2 Chains: B, E
Molecule details ›
Chains: B, E
Length: 83 amino acids
Theoretical weight: 9.48 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: NEW P61956 (Residues: 15-93; Coverage: 83%)
Gene names: SMT3B, SMT3H2, SUMO2
Sequence domains: Ubiquitin-2 like Rad60 SUMO-like
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Ran GTPase-activating protein 1 Chains: C, F
Molecule details ›
Chains: C, F
Length: 171 amino acids
Theoretical weight: 18.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: NEW P46060 (Residues: 418-587; Coverage: 29%)
Gene names: KIAA1835, RANGAP1, SD
Structure domains: Ran-GTPase activating protein 1, C-terminal domain
E3 SUMO-protein ligase ZNF451 Chain: G
Molecule details ›
Chain: G
Length: 65 amino acids
Theoretical weight: 6.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: NEW Q9Y4E5 (Residues: 2-56; Coverage: 5%)
Gene names: COASTER, KIAA0576, KIAA1702, ZNF451

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P212121
Unit cell:
a: 78.24Å b: 115.06Å c: 130.98Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.195 0.234
Expression system: Escherichia coli BL21(DE3)