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

X-ray diffraction
3.01Å resolution
PDB entry 1z5s coloured by chain, front view.
PDB entry 1z5s coloured by chain, side view.
PDB entry 1z5s coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero tetramer (preferred)
Entry contents: 4 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: E3 ligase (RANBP2) complex and Small ubiquitin-related modifier 1
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Multimeric state: hetero tetramer
Accessible surface area: 22357.91 Å2
Buried surface area: 6216.13 Å2
Dissociation area: 586.5 Å2
Dissociation energy (ΔGdiss): -3.33 kcal/mol
Dissociation entropy (TΔSdiss): 12.03 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-155409

Macromolecules

SUMO-conjugating enzyme UBC9
Chain: A
Length: 158 amino acids
Theoretical weight: 18.03 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P63279 (Residues: 1-158; Coverage: 100%)
Gene names: UBC9, UBCE9, UBE2I
Pfam: Ubiquitin-conjugating enzyme
InterPro:
CATH: Ubiquitin Conjugating Enzyme
SCOP: UBC-related
SUMO-conjugating enzyme UBC9 in PDB entry 1z5s, assembly 1, front view.
SUMO-conjugating enzyme UBC9 in PDB entry 1z5s, assembly 1, side view.
SUMO-conjugating enzyme UBC9 in PDB entry 1z5s, assembly 1, top view.
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Small ubiquitin-related modifier 1
Chain: B
Length: 82 amino acids
Theoretical weight: 9.47 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
Pfam: Ubiquitin-2 like Rad60 SUMO-like
InterPro:
CATH: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
SCOP: Ubiquitin-related
Small ubiquitin-related modifier 1 in PDB entry 1z5s, assembly 1, front view.
Small ubiquitin-related modifier 1 in PDB entry 1z5s, assembly 1, side view.
Small ubiquitin-related modifier 1 in PDB entry 1z5s, assembly 1, top view.
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Ran GTPase-activating protein 1
Chain: C
Length: 172 amino acids
Theoretical weight: 18.69 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P46060 (Residues: 418-587; Coverage: 29%)
Gene names: KIAA1835, RANGAP1, SD
Pfam: RanGAP1 C-terminal domain
InterPro:
CATH: Ran-GTPase activating protein 1, C-terminal domain
SCOP: Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain
Ran GTPase-activating protein 1 in PDB entry 1z5s, assembly 1, front view.
Ran GTPase-activating protein 1 in PDB entry 1z5s, assembly 1, side view.
Ran GTPase-activating protein 1 in PDB entry 1z5s, assembly 1, top view.
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E3 SUMO-protein ligase RanBP2
Chain: D
Length: 83 amino acids
Theoretical weight: 9.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P49792 (Residues: 2631-2711; Coverage: 3%)
Gene names: NUP358, RANBP2
Pfam: Nup358/RanBP2 E3 ligase domain
InterPro: Nup358/RanBP2 E3 ligase domain
E3 SUMO-protein ligase RanBP2 in PDB entry 1z5s, assembly 1, front view.
E3 SUMO-protein ligase RanBP2 in PDB entry 1z5s, assembly 1, side view.
E3 SUMO-protein ligase RanBP2 in PDB entry 1z5s, assembly 1, top view.
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