9GW9 | pdb_00009gw9

Cryo-EM structure of Gephyrin E domain filament interface


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9GW9

This is version 1.1 of the entry. See complete history

Literature

Gephyrin filaments represent the molecular basis of inhibitory postsynaptic densities.

Macha, A.Liebsch, F.Bruckisch, E.H.W.Burdina, N.von Stulpnagel, I.Benting, K.Gunkel, M.Behrmann, E.Schwarz, G.

(2025) Nat Commun 16: 8293-8293

  • DOI: https://doi.org/10.1038/s41467-025-63748-w
  • Primary Citation Related Structures: 
    9GW9

  • PubMed Abstract: 

    The multifunctional protein gephyrin clusters inhibitory receptors at the postsynaptic membrane in the CNS. Gephyrin has been proposed to form the inhibitory postsynaptic density by liquid-liquid phase separation, involving a complex interplay between receptor binding and oligomerization via its conserved G- and E-domains. Here we show by single particle cryo-EM analysis that dimerization promotes the formation of gephyrin filaments in which two E-domain dimers are linked by Z-shaped interfaces formed between two subdomains II (SDII) of adjacent dimers. Deletion of SDII, introduction of two epilepsy-causing pathogenic variants, or neutralization of an opposing charge in the interface abolish the formation of filaments, in vitro phase separation, and synaptic receptor clustering in hippocampal neurons. In conclusion, this work identifies gephyrin E-domain filaments as the structural foundation underlying gephyrin both phase separation and receptor clustering at inhibitory postsynaptic densities.


  • Organizational Affiliation
    • Institute of Biochemistry, Department of Chemistry and Biochemistry, University of Cologne, Cologne, Germany.

Macromolecule Content 

  • Total Structure Weight: 139.92 kDa 
  • Atom Count: 6,105 
  • Modeled Residue Count: 819 
  • Deposited Residue Count: 1,284 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Gephyrin
A, B, C
428Rattus norvegicusMutation(s): 0 
Gene Names: GphnGph
EC: 2.7.7.75 (PDB Primary Data), 2.10.1.1 (PDB Primary Data)
UniProt
Find proteins for Q03555 (Rattus norvegicus)
Explore Q03555 
Go to UniProtKB:  Q03555
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ03555
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4
MODEL REFINEMENTPHENIX1.21-5207

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyINST 216/949-1 FUGG
German Research Foundation (DFG)GermanyINST 216/512/1 FUGG

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2026-04-22
    Changes: Data collection, Database references