9GW9 | pdb_00009gw9

Cryo-EM structure of Gephyrin E domain filament interface

• PDB DOI: https://doi.org/10.2210/pdb9GW9/pdb
• EM Map EMD-51644: EMDB EMDataResource

• Classification: PROTEIN BINDING
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-09-26 Released: 2025-10-08 
• Deposition Author(s): Macha, A., Gunkel, M., Schwarz, G., Behrmann, E., Burdina, N.
• Funding Organization(s): German Research Foundation (DFG)

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Experimental Data Snapshot

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

Starting Model: experimental

Literature

Cryo-EM structure of Gephyrin E domain filament interface

Macha, A., Gunkel, M., Schwarz, G., Behrmann, E., Burdina, N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gephyrin	A, B, C	428	Rattus norvegicus	Mutation(s): 0  Gene Names: Gphn, Gph 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

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.4
MODEL REFINEMENT	PHENIX	1.21-5207

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-08 
Deposition Author(s): Macha, A., Gunkel, M., Schwarz, G., Behrmann, E., Burdina, N.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	INST 216/949-1 FUGG
German Research Foundation (DFG)	Germany	INST 216/512/1 FUGG

Revision History  

• Version 1.0: 2025-10-08
  Type: Initial release