› 5d2m

X-ray diffraction
2.4Å resolution

Complex between human SUMO2-RANGAP1, UBC9 and ZNF451

Released:
DOI: 10.2210/pdb5d2m/pdb
PDB entry 5d2m coloured by chain, front view.
PDB entry 5d2m coloured by chain, side view.
PDB entry 5d2m coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for catalytic activation by the human ZNF451 SUMO E3 ligase.
Cappadocia L, Pichler A, Lima CD
Nat Struct Mol Biol 22 968-75 (2015)
PMID: 26524494

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero pentamer (preferred)
hetero dimer
PDBe Complex ID:
PDB-CPX-155410 (preferred)
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: 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: 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: P46060 (Residues: 418-587; Coverage: 29%)
Gene names: KIAA1835, RANGAP1, SD
Sequence domains: RanGAP1 C-terminal domain
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: Q9Y4E5 (Residues: 2-56; Coverage: 5%)
Gene names: COASTER, KIAA0576, KIAA1702, ZNF451

Ligands and Environments

1 bound ligand:
Ligand EDO 5 x EDO
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)

Quick links

Citations

24 review citations

The post-translational modification, SUMOylation, and cancer (Review).
Han et al. (2018)
23 more

12 mentions without citation

Ubiquitin-like Protein Conjugation: Structures, Chemistry, and Mechanism.
Cappadocia et al. (2018)
11 more