4NPN

Crystal structure of human tetra-SUMO-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.633 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain.

Kung, C.C.-H.Naik, M.T.Wang, S.H.Shih, H.M.Chang, C.C.Lin, L.Y.Chen, C.L.Ma, C.Chang, C.F.Huang, T.H.

(2014) Biochem.J. 462: 53-65

  • DOI: 10.1042/BJ20140521

  • PubMed Abstract: 
  • The E3 ubiquitin ligase RNF4 (RING finger protein 4) contains four tandem SIM [SUMO (small ubiquitin-like modifier)-interaction motif] repeats for selective interaction with poly-SUMO-modified proteins, which it targets for degradation. We employed a ...

    The E3 ubiquitin ligase RNF4 (RING finger protein 4) contains four tandem SIM [SUMO (small ubiquitin-like modifier)-interaction motif] repeats for selective interaction with poly-SUMO-modified proteins, which it targets for degradation. We employed a multi-faceted approach to characterize the structure of the RNF4-SIMs domain and the tetra-SUMO2 chain to elucidate the interaction between them. In solution, the SIM domain was intrinsically disordered and the linkers of the tetra-SUMO2 were highly flexible. Individual SIMs of the RNF4-SIMs domains bind to SUMO2 in the groove between the β2-strand and the α1-helix parallel to the β2-strand. SIM2 and SIM3 bound to SUMO with a high affinity and together constituted the recognition module necessary for SUMO binding. SIM4 alone bound to SUMO with low affinity; however, its contribution to tetra-SUMO2 binding avidity is comparable with that of SIM3 when in the RNF4-SIMs domain. The SAXS data of the tetra-SUMO2-RNF4-SIMs domain complex indicate that it exists as an ordered structure. The HADDOCK model showed that the tandem RNF4-SIMs domain bound antiparallel to the tetra-SUMO2 chain orientation and wrapped around the SUMO protamers in a superhelical turn without imposing steric hindrance on either molecule.


    Organizational Affiliation

    ¶Genomics Research Center, Academia Sinica, Taipei 11529, Taiwan.,*Institute of Biomedical Sciences, Academia Sinica, Taipei 11529, Taiwan.,§Scientific Instrument Center, Academia Sinica, Taipei 11529, Taiwan.,∥Graduate Institute of Translational Medicine, Taipei Medical University, Taipei 110, Taiwan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Small ubiquitin-related modifier 2
A
102Homo sapiensMutation(s): 0 
Gene Names: SUMO2 (SMT3B, SMT3H2)
Find proteins for P61956 (Homo sapiens)
Go to Gene View: SUMO2
Go to UniProtKB:  P61956
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.633 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.198 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 75.123α = 90.00
b = 75.123β = 90.00
c = 33.116γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
SOLVEphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-15
    Type: Initial release