› 3uip

X-ray diffraction
2.29Å resolution

Complex between human RanGAP1-SUMO1, UBC9 and the IR1 domain from RanBP2 containing IR2 Motif II

Released:
DOI: 10.2210/pdb3uip/pdb
PDB entry 3uip coloured by chain, front view.
PDB entry 3uip coloured by chain, side view.
PDB entry 3uip coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Determinants of small ubiquitin-like modifier 1 (SUMO1) protein specificity, E3 ligase, and SUMO-RanGAP1 binding activities of nucleoporin RanBP2.
Gareau JR, Reverter D, Lima CD
J Biol Chem 287 4740-51 (2012)
PMID: 22194619

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-155409 (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: 18.14 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 1 Chain: B
Molecule details ›
Chain: B
Length: 80 amino acids
Theoretical weight: 9.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: 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: 171 amino acids
Theoretical weight: 18.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P46060 (Residues: 419-587; 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 RanBP2 Chain: D
Molecule details ›
Chain: D
Length: 67 amino acids
Theoretical weight: 7.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P49792 (Residues: 2631-2695; Coverage: 2%)
Gene names: NUP358, RANBP2
Sequence domains: Nup358/RanBP2 E3 ligase domain

Ligands and Environments

No bound ligands
2 modified residues:
Ligand CSD 1 x CSD
Ligand CME 2 x CME

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: C2221
Unit cell:
a: 136.651Å b: 199.187Å c: 63.411Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.192 0.232
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

7 review citations

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

10 mentions without citation

Emerging roles of sumoylation in the regulation of actin, microtubules, intermediate filaments, and septins.
Alonso et al. (2015)
9 more