9S3F

Cryo-EM structure of Gephyrin in complex with Darpin 27F3, revealing linker-E domain interactions

Summary for 9S3F

• Entry DOI: 10.2210/pdb9s3f/pdb
• EMDB information: 54532
• Descriptor: Isoform 5 of Gephyrin, Darpin 27F3 (2 entities in total)
• Functional Keywords: scaffolding protein, postsynaptic density, protein-protein interaction, linker-mediated regulation, structural protein
• Biological source: Rattus norvegicus (Norway rat); More
• Total number of polymer chains: 3
• Total formula weight: 183223.55

Authors

Ortiz-Lopez, D.,Hove, T.,Schindelin, H.,Boettcher, B. (deposition date: 2025-07-24, release date: 2026-06-24)

Primary citation

Ortiz-Lopez, D.,Hove, T.T.,Huhn, C.,Camuso, S.,van Gen Hassend, P.M.,Sander, B.,Campbell, B.F.N.,Tyagarajan, S.K.,Pluckthun, A.,Specht, C.G.,Maric, H.M.,Bottcher, B.,Schindelin, H.
Cryo-EM structures of higher order Gephyrin oligomers reveal principles of inhibitory postsynaptic scaffold organization.
Nat Commun, 17:-, 2026

PubMed Abstract: Gephyrin, the principal scaffolding protein of inhibitory postsynaptic densities, clusters glycine and GABA receptors via multivalent interactions. It features structured N and C terminal domains connected by an intrinsically disordered linker. Although the structural and functional properties of its terminal domains are well characterized, the mechanism by which full-length gephyrin organizes into higher-order complexes remains unresolved. Here, we combine biochemical reconstitution, cryo-electron microscopy, and mutational analyses to elucidate the structural logic of gephyrin oligomerization. We demonstrate that gephyrin adopts a stable dimeric assembly which constitutes the basic unit for both linear and oblique tetramers as well as linear hexameric arrangements. High resolution structures reveal a critical segment of the flexible linker that adopts two distinct conformations, one of which occludes the receptor-binding site. This segment harbors key phosphorylation sites, suggesting a regulatory control mechanism. Our findings redefine the architecture of inhibitory postsynaptic sites and reconcile gephyrin oligomerization models with published in-situ postsynaptic densities characterized by cryo-electron tomography.

PubMed: 41991925
DOI: 10.1038/s41467-026-71771-8

Experimental method

ELECTRON MICROSCOPY (3.12 Å)