2FU3 | pdb_00002fu3

Crystal structure of gephyrin E-domain

• PDB DOI: https://doi.org/10.2210/pdb2FU3/pdb

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


• Deposited: 2006-01-25 Released: 2006-03-14 
• Deposition Author(s): Kim, E.Y., Schindelin, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.273 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.209 (DCC) 

Literature

Deciphering the structural framework of glycine receptor anchoring by gephyrin.

Kim, E.Y., Schrader, N., Smolinsky, B., Bedet, C., Vannier, C., Schwarz, G., Schindelin, H.

(2006) EMBO J 25: 1385-1395

• PubMed: 16511563 
• DOI: https://doi.org/10.1038/sj.emboj.7601029
• Primary Citation Related Structures: 
  2FTS, 2FU3


• PubMed Abstract: 
  

  Glycine is the major inhibitory neurotransmitter in the spinal cord and brain stem. Gephyrin is required to achieve a high concentration of glycine receptors (GlyRs) in the postsynaptic membrane, which is crucial for efficient glycinergic signal transduction. The interaction between gephyrin and the GlyR involves the E-domain of gephyrin and a cytoplasmic loop located between transmembrane segments three and four of the GlyR beta subunit. Here, we present crystal structures of the gephyrin E-domain with and without the GlyR beta-loop at 2.4 and 2.7 A resolutions, respectively. The GlyR beta-loop is bound in a symmetric 'key and lock' fashion to each E-domain monomer in a pocket adjacent to the dimer interface. Structure-guided mutagenesis followed by in vitro binding and in vivo colocalization assays demonstrate that a hydrophobic interaction formed by Phe 330 of gephyrin and Phe 398 and Ile 400 of the GlyR beta-loop is crucial for binding.

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Organizational Affiliation: 
• Department of Biochemistry, Center for Structural Biology, State University of New York, Stony Brook, NY 11794-5115, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 91.3 kDa 
• Atom Count: 6,257 
• Modeled Residue Count: 824 
• Deposited Residue Count: 838 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
gephyrin	A, B	419	Rattus norvegicus	Mutation(s): 0  Gene Names: Rattus norvegicus (Norway rat) EC: 2.10.1.1 (UniProt), 2.7.7.75 (UniProt)
UniProt
Find proteins for Q03555 (Rattus norvegicus) Explore Q03555  Go to UniProtKB:  Q03555

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.273 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.209 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.82	α = 90
b = 156.195	β = 90
c = 51.362	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-03-14 
Deposition Author(s): Kim, E.Y., Schindelin, H.

Revision History  

• Version 1.0: 2006-03-14
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references