8CDT

Crystal structure of the xNup93-Nb2t VHH antibody

Summary for 8CDT

• Entry DOI: 10.2210/pdb8cdt/pdb
• Descriptor: 15-Nup93 tracking VHH antibody, GLYCEROL (3 entities in total)
• Functional Keywords: vhh antibody, nanobody, immune system
• Biological source: Vicugna pacos (Alpaca)
• Total number of polymer chains: 1
• Total formula weight: 13105.83

Authors

Guttler, T.,Colom, M.S.,Gorlich, D. (deposition date: 2023-02-01, release date: 2024-02-21, Last modification date: 2024-10-23)

Primary citation

Sola Colom, M.,Fu, Z.,Gunkel, P.,Guttler, T.,Trakhanov, S.,Srinivasan, V.,Gregor, K.,Pleiner, T.,Gorlich, D.
A checkpoint function for Nup98 in nuclear pore formation suggested by novel inhibitory nanobodies.
Embo J., 43:2198-2232, 2024

PubMed Abstract: Nuclear pore complex (NPC) biogenesis is a still enigmatic example of protein self-assembly. We now introduce several cross-reacting anti-Nup nanobodies for imaging intact nuclear pore complexes from frog to human. We also report a simplified assay that directly tracks postmitotic NPC assembly with added fluorophore-labeled anti-Nup nanobodies. During interphase, NPCs are inserted into a pre-existing nuclear envelope. Monitoring this process is challenging because newly assembled NPCs are indistinguishable from pre-existing ones. We overcame this problem by inserting Xenopus-derived NPCs into human nuclear envelopes and using frog-specific anti-Nup nanobodies for detection. We further asked whether anti-Nup nanobodies could serve as NPC assembly inhibitors. Using a selection strategy against conserved epitopes, we obtained anti-Nup93, Nup98, and Nup155 nanobodies that block Nup-Nup interfaces and arrest NPC assembly. We solved structures of nanobody-target complexes and identified roles for the Nup93 α-solenoid domain in recruiting Nup358 and the Nup214·88·62 complex, as well as for Nup155 and the Nup98 autoproteolytic domain in NPC scaffold assembly. The latter suggests a checkpoint linking pore formation to the assembly of the Nup98-dominated permeability barrier.

PubMed: 38649536
DOI: 10.1038/s44318-024-00081-w

Experimental method

X-RAY DIFFRACTION (1.41 Å)