4NPN

Crystal structure of human tetra-SUMO-2

Summary for 4NPN

• Entry DOI: 10.2210/pdb4npn/pdb
• Related: 1WM2 1WM3 2RPQ 4BKG
• Descriptor: Small ubiquitin-related modifier 2 (2 entities in total)
• Functional Keywords: protein binding, protein transport
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: P61956
• Total number of polymer chains: 1
• Total formula weight: 11460.79

Authors

Kung, C.C.-H.,Naik, M.T.,Chen, C.L.,Ma, C.,Huang, T.H. (deposition date: 2013-11-22, release date: 2014-10-15, Last modification date: 2024-03-20)

Primary citation

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.
Structural analysis of poly-SUMO chain recognition by the RNF4-SIMs domain.
Biochem.J., 462:53-65, 2014

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 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.

PubMed: 24844634
DOI: 10.1042/BJ20140521

Experimental method

X-RAY DIFFRACTION (1.633 Å)