Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 91.30 kDa 
• Atom Count: 6257 
• Modelled Residue Count: 824 
• Deposited Residue Count: 838 
• Unique protein chains: 1

2FU3

Crystal structure of gephyrin E-domain

• PDB DOI: 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 
• R-Value Work: 0.202 

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: 10.1038/sj.emboj.7601029
• Primary Citation of 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.

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), Gphn, Gph EC: 2.7.7.75 (UniProt), 2.10.1.1 (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 
• R-Value Work: 0.202 
• 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

• Deposited Date: 2006-01-25 
• 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