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TitleCryo-EM structures of higher order Gephyrin oligomers reveal principles of inhibitory postsynaptic scaffold organization.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Year 2026
Publish dateApr 16, 2026
AuthorsDiego Ortiz-López / Tamsanqa T Hove / Christiane Huhn / Serena Camuso / Pia M van Gen Hassend / Bodo Sander / Benjamin F N Campbell / Shiva K Tyagarajan / Andreas Plückthun / Christian G Specht / Hans M Maric / Bettina Böttcher / Hermann Schindelin /
PubMed AbstractGephyrin, the principal scaffolding protein of inhibitory postsynaptic densities, clusters glycine and GABA receptors via multivalent interactions. It features structured N and C terminal domains ...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.
External linksNat Commun / PubMed:41991925 / PubMed Central
MethodsEM (single particle)
Resolution2.31 - 3.48 Å
Structure data

54532

9s3f

EMDB-54532, PDB-9s3f:
Cryo-EM structure of Gephyrin in complex with Darpin 27F3, revealing linker-E domain interactions
Method: EM (single particle) / Resolution: 3.12 Å

EMDB-54539: Gephyrin E-Domain dimer of dimers - Consensus Map
Method: EM (single particle) / Resolution: 3.48 Å

54540

9s3m

EMDB-54540, PDB-9s3m:
Cryo-EM structure of Gephyrin E domain in complex with Darpin 27F3
Method: EM (single particle) / Resolution: 2.31 Å

EMDB-54544: Gephyrin E-Domain dimer of dimers - local refinement of dimer A
Method: EM (single particle) / Resolution: 3.07 Å

EMDB-54545: Gephyrin E-Domain dimer of dimers - local refinement of dimer B
Method: EM (single particle) / Resolution: 3.1 Å

54551

9s3t

EMDB-54551, PDB-9s3t:
Gephyrin dimer of dimers - combined CryoEM map
Method: EM (single particle) / Resolution: 3.48 Å

Source
  • rattus norvegicus (Norway rat)
  • synthetic construct (others)
KeywordsSTRUCTURAL PROTEIN / scaffolding protein / postsynaptic density / protein-protein interaction / linker-mediated regulation / STRUCTURAL PROTEIN.

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