3H7P

Crystal structure of K63-linked di-ubiquitin

Summary for 3H7P

• Entry DOI: 10.2210/pdb3h7p/pdb
• Related: 3H7S
• Descriptor: Ubiquitin, CADMIUM ION, ... (4 entities in total)
• Functional Keywords: ubiquitin, isopeptide, k63-linked, polyubiquitin, cytoplasm, isopeptide bond, nucleus, phosphoprotein, ubl conjugation, signaling protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 17968.55

Authors

Weeks, S.D.,Grasty, K.C.,Hernandez-Cuebas, L.,Loll, P.J. (deposition date: 2009-04-28, release date: 2009-09-22, Last modification date: 2024-02-21)

Primary citation

Weeks, S.D.,Grasty, K.C.,Hernandez-Cuebas, L.,Loll, P.J.
Crystal structures of Lys-63-linked tri- and di-ubiquitin reveal a highly extended chain architecture.
Proteins, 77:753-759, 2009

PubMed Abstract: The covalent attachment of different types of poly-ubiquitin chains signal different outcomes for the proteins so targeted. For example, a protein modified with Lys-48-linked poly-ubiquitin chains is targeted for proteasomal degradation, whereas Lys-63-linked chains encode nondegradative signals. The structural features that enable these different types of chains to encode different signals have not yet been fully elucidated. We report here the X-ray crystal structures of Lys-63-linked tri- and di-ubiquitin at resolutions of 2.3 and 1.9 A, respectively. The tri- and di-ubiquitin species adopt essentially identical structures. In both instances, the ubiquitin chain assumes a highly extended conformation with a left-handed helical twist; the helical chain contains four ubiquitin monomers per turn and has a repeat length of approximately 110 A. Interestingly, Lys-48 ubiquitin chains also adopt a left-handed helical structure with a similar repeat length. However, the Lys-63 architecture is much more open than that of Lys-48 chains and exposes much more of the ubiquitin surface for potential recognition events. These new crystal structures are consistent with the results of solution studies of Lys-63 chain conformation, and reveal the structural basis for differential recognition of Lys-63 versus Lys-48 chains.

PubMed: 19731378
DOI: 10.1002/prot.22568

Experimental method

X-RAY DIFFRACTION (1.9 Å)