1Z5S

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex.

Reverter, D., Lima, C.D.

(2005) Nature 435: 687-692

  • DOI: 10.1038/nature03588
  • Primary Citation of Related Structures:  
    1Z5S

  • PubMed Abstract: 

    • SUMO-1 (for small ubiquitin-related modifier) belongs to the ubiquitin (Ub) and ubiquitin-like (Ubl) protein family. SUMO conjugation occurs on specific lysine residues within protein targets, regulating pathways involved in differentiation, apoptosis, the cell cycle and responses to stress by altering protein function through changes in activity or cellular localization or by protecting substrates from ubiquitination ...

    SUMO-1 (for small ubiquitin-related modifier) belongs to the ubiquitin (Ub) and ubiquitin-like (Ubl) protein family. SUMO conjugation occurs on specific lysine residues within protein targets, regulating pathways involved in differentiation, apoptosis, the cell cycle and responses to stress by altering protein function through changes in activity or cellular localization or by protecting substrates from ubiquitination. Ub/Ubl conjugation occurs in sequential steps and requires the concerted action of E2 conjugating proteins and E3 ligases. In addition to being a SUMO E3, the nucleoporin Nup358/RanBP2 localizes SUMO-conjugated RanGAP1 to the cytoplasmic face of the nuclear pore complex by means of interactions in a complex that also includes Ubc9, the SUMO E2 conjugating protein. Here we describe the 3.0-A crystal structure of a four-protein complex of Ubc9, a Nup358/RanBP2 E3 ligase domain (IR1-M) and SUMO-1 conjugated to the carboxy-terminal domain of RanGAP1. Structural insights, combined with biochemical and kinetic data obtained with additional substrates, support a model in which Nup358/RanBP2 acts as an E3 by binding both SUMO and Ubc9 to position the SUMO-E2-thioester in an optimal orientation to enhance conjugation.

    Organizational Affiliation: 

    Structural Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 IA158Homo sapiensMutation(s): 0 
Gene Names: UBE2I, UBC9, UBCE9
EC: 6.3.2.19 (PDB Primary Data), 2.3.2 (UniProt)
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Find proteins for P63279 (Homo sapiens)
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PHAROS:  P63279
GTEx:  ENSG00000103275 
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UniProt GroupP63279
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like protein SMT3CB82Homo sapiensMutation(s): 0 
Gene Names: UBL1, SMT3C, SMT3H3, SUMO1, OK/SW-cl.43
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Find proteins for P63165 (Homo sapiens)
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GTEx:  ENSG00000116030 
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UniProt GroupP63165
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ran GTPase-activating protein 1C172Homo sapiensMutation(s): 0 
Gene Names: RANGAP1, KIAA1835, SD
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GTEx:  ENSG00000100401 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Ran-binding protein 2D83Homo sapiensMutation(s): 0 
Gene Names: RANBP2, NUP358
EC: 2.3.2
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Find proteins for P49792 (Homo sapiens)
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PHAROS:  P49792
GTEx:  ENSG00000153201 
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UniProt GroupP49792
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.123α = 90
b = 157.123β = 90
c = 59.613γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance