2UYZ

Non-covalent complex between Ubc9 and SUMO1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Noncovalent interaction between Ubc9 and SUMO promotes SUMO chain formation.

Knipscheer, P.van Dijk, W.J.Olsen, J.V.Mann, M.Sixma, T.K.

(2007) EMBO J 26: 2797-2807

  • DOI: 10.1038/sj.emboj.7601711
  • Primary Citation of Related Structures:  
    2UYZ

  • PubMed Abstract: 
  • The ubiquitin-related modifier SUMO regulates a wide range of cellular processes by post-translational modification with one, or a chain of SUMO molecules. Sumoylation is achieved by the sequential action of several enzymes in which the E2, Ubc9, tra ...

    The ubiquitin-related modifier SUMO regulates a wide range of cellular processes by post-translational modification with one, or a chain of SUMO molecules. Sumoylation is achieved by the sequential action of several enzymes in which the E2, Ubc9, transfers SUMO from the E1 to the target mostly with the help of an E3 enzyme. In this process, Ubc9 not only forms a thioester bond with SUMO, but also interacts with SUMO noncovalently. Here, we show that this noncovalent interaction promotes the formation of short SUMO chains on targets such as Sp100 and HDAC4. We present a crystal structure of the noncovalent Ubc9-SUMO1 complex, showing that SUMO is located far from the E2 active site and resembles the noncovalent interaction site for ubiquitin on UbcH5c and Mms2. Structural comparison suggests a model for poly-sumoylation involving a mechanism analogous to Mms2-Ubc13-mediated ubiquitin chain formation.


    Organizational Affiliation

    Department of Molecular Carcinogenesis, The Netherlands Cancer Institute and Center for Biomedical Genetics, Plesmanlaan, Amsterdam, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SUMO-CONJUGATING ENZYME UBC9A158Mus musculusMutation(s): 1 
Gene Names: Ube2iUbc9Ubce2iUbce9
EC: 6.3.2.19 (PDB Primary Data), 2.3.2 (UniProt)
Find proteins for P63280 (Mus musculus)
Explore P63280 
Go to UniProtKB:  P63280
NIH Common Fund Data Resources
IMPC  MGI:107365
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SMALL UBIQUITIN-RELATED MODIFIER 1B79Homo sapiensMutation(s): 0 
Gene Names: SUMO1SMT3CSMT3H3UBL1OK/SW-cl.43
Find proteins for P63165 (Homo sapiens)
Explore P63165 
Go to UniProtKB:  P63165
NIH Common Fund Data Resources
PHAROS  P63165
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.481α = 90
b = 35.03β = 93.41
c = 72.915γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-12
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-28
    Changes: Database references, Source and taxonomy, Structure summary