PDBe 1z5s

X-ray diffraction
3.01Å resolution

Crystal structure of a complex between UBC9, SUMO-1, RANGAP1 and NUP358/RANBP2

Released:
Source organism: Homo sapiens

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
SUMO-conjugating enzyme UBC9 Chain: A
Molecule details ›
Chain: A
Length: 158 amino acids
Theoretical weight: 18.03 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 1 Chain: B
Molecule details ›
Chain: B
Length: 82 amino acids
Theoretical weight: 9.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: NEW P63165 (Residues: 18-97; Coverage: 79%)
Gene names: OK/SW-cl.43, SMT3C, SMT3H3, SUMO1, UBL1
Sequence domains: Ubiquitin-2 like Rad60 SUMO-like
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Ran GTPase-activating protein 1 Chain: C
Molecule details ›
Chain: C
Length: 172 amino acids
Theoretical weight: 18.69 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 RanBP2 Chain: D
Molecule details ›
Chain: D
Length: 83 amino acids
Theoretical weight: 9.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: NEW P49792 (Residues: 2631-2711; Coverage: 3%)
Gene names: NUP358, RANBP2
Sequence domains: Nup358/RanBP2 E3 ligase domain

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 31-ID
Spacegroup: P3221
Unit cell:
a: 157.123Å b: 157.123Å c: 59.613Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.247 0.247 0.29
Expression system: Escherichia coli BL21(DE3)