Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13

Mol Cell. 2009 Aug 14;35(3):280-90. doi: 10.1016/j.molcel.2009.06.010.


Degradation by the proteasome typically requires substrate ubiquitination. Two ubiquitin receptors exist in the proteasome, S5a/Rpn10 and Rpn13. Whereas Rpn13 has only one ubiquitin-binding surface, S5a binds ubiquitin with two independent ubiquitin-interacting motifs (UIMs). Here, we use nuclear magnetic resonance (NMR) and analytical ultracentrifugation to define at atomic level resolution how S5a binds K48-linked diubiquitin, in which K48 of one ubiquitin subunit (the "proximal" one) is covalently bonded to G76 of the other (the "distal" subunit). We demonstrate that S5a's UIMs bind the two subunits simultaneously with a preference for UIM2 binding to the proximal subunit while UIM1 binds to the distal one. In addition, NMR experiments reveal that Rpn13 and S5a bind K48-linked diubiquitin simultaneously with subunit specificity, and a model structure of S5a and Rpn13 bound to K48-linked polyubiquitin is provided. Altogether, our data demonstrate that S5a is highly adaptive and cooperative toward binding ubiquitin chains.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Binding Sites
  • Humans
  • Intracellular Signaling Peptides and Proteins
  • Membrane Glycoproteins / metabolism*
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular
  • Proteasome Endopeptidase Complex / chemistry
  • Proteasome Endopeptidase Complex / metabolism*
  • Protein Structure, Tertiary
  • Protein Subunits / chemistry
  • Protein Subunits / metabolism
  • RNA-Binding Proteins
  • Ubiquitin / chemistry
  • Ubiquitin / metabolism*
  • Ubiquitination
  • Ultracentrifugation


  • ADRM1 protein, human
  • Intracellular Signaling Peptides and Proteins
  • Membrane Glycoproteins
  • PSMD4 protein, human
  • Protein Subunits
  • RNA-Binding Proteins
  • Ubiquitin
  • Proteasome Endopeptidase Complex

Associated data

  • PDB/2KDE
  • PDB/2KDF