2KDE: NMR structure of major S5a (196-306):K48 linked diubiquitin species

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.
PDB ID: 2KDEDownload
MMDB ID: 76367
PDB Deposition Date: 2009/1/6
Updated in MMDB: 2009/09
Experimental Method:
solution nmr
Source Organism:
Homo sapiens
Similar Structures:
Molecular Components in 2KDE
Label Count Molecule
Proteins (3 molecules)
26S Proteasome Non-atpase Regulatory Subunit 4(Gene symbol: PSMD4)
Molecule annotation
Ubiquitin(Gene symbol: LOC100190766)
Molecule annotation
* Click molecule labels to explore molecular sequence information.

Citing MMDB