8QW4

FZD3 in complex with nanobody 9

Summary for 8QW4

• Entry DOI: 10.2210/pdb8qw4/pdb
• EMDB information: 18680
• Descriptor: Frizzled-3, Nanobody Nb9 (2 entities in total)
• Functional Keywords: fzd3 nanobody, cell adhesion
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 74643.93

Authors

Zhao, Y.,Jones, E.Y. (deposition date: 2023-10-18, release date: 2024-09-04, Last modification date: 2024-10-23)

Primary citation

Hillier, J.,Zhao, Y.,Carrique, L.,Malinauskas, T.,Ruza, R.R.,Chang, T.H.,Yi, G.,Duyvesteyn, H.M.E.,Yu, J.,Lu, W.,Pardon, E.,Steyaert, J.,Zhu, Y.,Ni, T.,Jones, E.Y.
Structural insights into Frizzled3 through nanobody modulators.
Nat Commun, 15:7228-7228, 2024

PubMed Abstract: The Wnt receptor Frizzled3 (FZD3) is important for brain axonal development and cancer progression. We report structures of FZD3 in complex with extracellular and intracellular binding nanobodies (Nb). The crystal structure of Nb8 in complex with the FZD3 cysteine-rich domain (CRD) reveals that the nanobody binds at the base of the lipid-binding groove and can compete with Wnt5a. Nb8 fused with the Dickkopf-1 C-terminal domain behaves as a FZD3-specific Wnt surrogate, activating β-catenin signalling. The cryo-EM structure of FZD3 in complex with Nb9 reveals partially resolved density for the CRD, which exhibits positional flexibility, and a transmembrane conformation that resembles active GPCRs. Nb9 binds to the cytoplasmic region of FZD3 at the putative Dishevelled (DVL) or G protein-binding site, competes with DVL binding, and inhibits GαS coupling. In combination, our FZD3 structures with nanobody modulators map extracellular and intracellular interaction surfaces of functional, and potentially therapeutic, relevance.

PubMed: 39174501
DOI: 10.1038/s41467-024-51451-1

Experimental method

ELECTRON MICROSCOPY (2.9 Å)