6X07

Nic96 from S. cerevisiae bound by VHH-SAN12

Summary for 6X07

• Entry DOI: 10.2210/pdb6x07/pdb
• Descriptor: Nucleoporin NIC96, VHH-SAN12 (3 entities in total)
• Functional Keywords: nucleoporin, nanobody, structural protein
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Total number of polymer chains: 2
• Total formula weight: 91001.16

Authors

Andersen, K.,Nordeen, S.A.,Schwartz, T.U. (deposition date: 2020-05-15, release date: 2020-12-09, Last modification date: 2023-10-18)

Primary citation

Nordeen, S.A.,Andersen, K.R.,Knockenhauer, K.E.,Ingram, J.R.,Ploegh, H.L.,Schwartz, T.U.
A nanobody suite for yeast scaffold nucleoporins provides details of the nuclear pore complex structure.
Nat Commun, 11:6179-6179, 2020

PubMed Abstract: Nuclear pore complexes (NPCs) are the main conduits for molecular exchange across the nuclear envelope. The NPC is a modular assembly of ~500 individual proteins, called nucleoporins or nups. Most scaffolding nups are organized in two multimeric subcomplexes, the Nup84 or Y complex and the Nic96 or inner ring complex. Working in S. cerevisiae, and to study the assembly of these two essential subcomplexes, we here develop a set of twelve nanobodies that recognize seven constituent nucleoporins of the Y and Nic96 complexes. These nanobodies all bind specifically and with high affinity. We present structures of several nup-nanobody complexes, revealing their binding sites. Additionally, constitutive expression of the nanobody suite in S. cerevisiae detect accessible and obstructed surfaces of the Y complex and Nic96 within the NPC. Overall, this suite of nanobodies provides a unique and versatile toolkit for the study of the NPC.

PubMed: 33268786
DOI: 10.1038/s41467-020-19884-6

Experimental method

X-RAY DIFFRACTION (2.1 Å)