4NPN : Crystal structure of human tetra-SUMO-2

  • Mandar T. Naik (Contributor)
  • Camy C H Kung (Contributor)
  • Chia Lin Chen (Contributor)
  • Che Ma (Contributor)
  • Tai-huang Huang (Contributor)

Dataset

Description

Experimental Technique/Method:X-RAY DIFFRACTION
Resolution:1.63
Classification:PROTEIN TRANSPORT
Release Date:2014-10-15
Deposition Date:2013-11-22
Revision Date:
Molecular Weight:11460.79
Macromolecule Type:Protein
Residue Count:102
Atom Site Count:575
DOI:10.2210/pdb4npn/pdb

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 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.
Date made available2014 Oct 15
PublisherUnknown Publisher

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