7UPM image
Entry Detail
PDB ID:
7UPM
Title:
Tribbles (TRIB2) pseudokinase bound to nanobody Nb4.103
Biological Source:
Host Organism:
PDB Version:
Deposition Date:
2022-04-15
Release Date:
2022-09-14
Method Details:
Experimental Method:
Resolution:
2.70 Å
R-Value Free:
0.25
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 65 2 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Tribbles homolog 2
Chain IDs:A
Chain Length:264
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Nb4.103 Nanobody
Chain IDs:B
Chain Length:122
Number of Molecules:1
Biological Source:synthetic construct
Primary Citation
Nanobodies identify an activated state of the TRIB2 pseudokinase.
Structure 30 1518 ? (2022)
PMID: 36108635 DOI: 10.1016/j.str.2022.08.006

Abstact

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.

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