9SI7

Crystal structure of TBC domain of human TBC1D17

Summary for 9SI7

• Entry DOI: 10.2210/pdb9si7/pdb
• Descriptor: TBC1 domain family member 17 (2 entities in total)
• Functional Keywords: gtp-ase activating protein, rab-gap, protein binding
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 73680.60

Authors

Nielipinska, D.,Nielipinski, M.,Sekula, B.,Pietrzyk-Brzezinska, A.J. (deposition date: 2025-08-28, release date: 2026-05-06)

Primary citation

Nielipinska, D.,Orlikowska, M.,Nielipinski, M.,Sekula, B.,Blazewska, K.M.,Gendaszewska-Darmach, E.,Pietrzyk-Brzezinska, A.J.
Structural and functional insights into TBC1D17 highlight the importance of the previously uncharacterized Rab-binding domain.
Protein Sci., 35:e70581-e70581, 2026

PubMed Abstract: TBC (Tre2/Bub2/Cdc16) domain-containing proteins constitute the widespread family of GTPase-activating proteins (GAPs). They interact with the Rab superfamily of small GTPases, stimulate GTP hydrolysis, and regulate vesicle trafficking. TBC1D17, involved in Shiga toxin trafficking, autophagy and glucose metabolism regulation, constitutes an example of GAP interacting with Rabs. Here we present the first crystal structures of the murine and human TBC domains of TBC1D17 proteins determined at 2.20 and 3.34 Å resolution, respectively. The TBC domain in both structures represents a heart-like shape. Our analyses revealed dimerization of the TBC domain through a fragment located near residues participating in GTP hydrolysis, a result we observed also in structures of closely related homologs. Furthermore, we tested Rab5a interactions with various fragments of TBC1D17. Interestingly, this protein contains an annotated, yet uncharacterized, Rab-binding domain (RBD) and our studies revealed strong interactions of Rab5a with TBC1D17 fragments containing RBD, while interactions with the TBC domain alone are much weaker. These results provide the first direct evidence for the critical role of the TBC1D17 RBD in interactions with Rab5a.

PubMed: 41999088
DOI: 10.1002/pro.70581

Experimental method

X-RAY DIFFRACTION (3.34 Å)