7UPM

Tribbles (TRIB2) pseudokinase bound to nanobody Nb4.103

Summary for 7UPM

• Entry DOI: 10.2210/pdb7upm/pdb
• Descriptor: Tribbles homolog 2, Nb4.103 Nanobody (3 entities in total)
• Functional Keywords: tribbles, psuedokinase, trb2, trib2, nanobody, signaling protein, signaling protein-immune system complex, signaling protein/immune system
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 42991.62

Authors

Jamieson, S.A.,Mace, P.D. (deposition date: 2022-04-15, release date: 2022-09-14, Last modification date: 2023-10-18)

Primary citation

Jamieson, S.A.,Pudjihartono, M.,Horne, C.R.,Viloria, J.S.,Dunlop, J.L.,McMillan, H.D.,Day, R.C.,Keeshan, K.,Murphy, J.M.,Mace, P.D.
Nanobodies identify an activated state of the TRIB2 pseudokinase.
Structure, 30:1518-, 2022

PubMed Abstract: Tribbles proteins (TRIB1-3) are pseudokinases that recruit substrates to the COP1 ubiquitin ligase. TRIB2 was the first Tribbles ortholog to be implicated as a myeloid leukemia oncogene, because it recruits the C/EBPα transcription factor for ubiquitination by COP1. Here we report identification of nanobodies that bind the TRIB2 pseudokinase domain with low nanomolar affinity. A crystal structure of the TRIB2-Nb4.103 complex identified the nanobody to bind the N-terminal lobe of TRIB2, enabling specific recognition of TRIB2 in an activated conformation that is similar to the C/EBPα-bound state of TRIB1. Characterization in solution revealed that Nb4.103 can stabilize a TRIB2 pseudokinase domain dimer in a face-to-face manner. Conversely, a distinct nanobody (Nb4.101) binds through a similar epitope but does not readily promote dimerization. In combination, this study identifies features of TRIB2 that could be exploited for the development of inhibitors and nanobody tools for future investigation of TRIB2 function.

PubMed: 36108635
DOI: 10.1016/j.str.2022.08.006

Experimental method

X-RAY DIFFRACTION (2.7 Å)