2KDF

NMR structure of minor S5a (196-306):K48 linked diubiquitin species

Summary for 2KDF

• Entry DOI: 10.2210/pdb2kdf/pdb
• Related: 1D3Z 1YX4 1YX5 1YX6 2KDE
• Descriptor: 26S proteasome non-ATPase regulatory subunit 4, Ubiquitin (2 entities in total)
• Functional Keywords: protein complex, ubiquitin interacting motifs, cytoplasm, nucleus, phosphoprotein, ubl conjugation, alternative splicing, proteasome, protein binding
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 3
• Total formula weight: 28980.54

Authors

Zhang, N.,Wang, Q.,Ehlinger, A.,Randles, L.,Lary, J.W.,Kang, Y.,Haririnia, A.,Cole, J.L.,Fushman, D.,Walters, K.J. (deposition date: 2009-01-06, release date: 2009-09-01, Last modification date: 2024-10-30)

Primary citation

Zhang, N.,Wang, Q.,Ehlinger, A.,Randles, L.,Lary, J.W.,Kang, Y.,Haririnia, A.,Storaska, A.J.,Cole, J.L.,Fushman, D.,Walters, K.J.
Structure of the s5a:k48-linked diubiquitin complex and its interactions with rpn13.
Mol.Cell, 35:280-290, 2009

PubMed Abstract: 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.

PubMed: 19683493
DOI: 10.1016/j.molcel.2009.06.010

Experimental method

SOLUTION NMR