1T3E

Structural basis of dynamic glycine receptor clustering


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of dynamic glycine receptor clustering by gephyrin

Sola, M.Bavro, V.N.Timmins, J.Franz, T.Ricard-Blum, S.Schoehn, G.Ruigrok, R.W.H.Paarmann, I.Saiyed, T.O'Sullivan, G.A.Schmitt, B.Betz, H.Weissenhorn, W.

(2004) Embo J. 23: 2510-2519

  • DOI: 10.1038/sj.emboj.7600256

  • PubMed Abstract: 
  • Gephyrin is a bi-functional modular protein involved in molybdenum cofactor biosynthesis and in postsynaptic clustering of inhibitory glycine receptors (GlyRs). Here, we show that full-length gephyrin is a trimer and that its proteolysis in vitro cau ...

    Gephyrin is a bi-functional modular protein involved in molybdenum cofactor biosynthesis and in postsynaptic clustering of inhibitory glycine receptors (GlyRs). Here, we show that full-length gephyrin is a trimer and that its proteolysis in vitro causes the spontaneous dimerization of its C-terminal region (gephyrin-E), which binds a GlyR beta-subunit-derived peptide with high and low affinity. The crystal structure of the tetra-domain gephyrin-E in complex with the beta-peptide bound to domain IV indicates how membrane-embedded GlyRs may interact with subsynaptic gephyrin. In vitro, trimeric full-length gephyrin forms a network upon lowering the pH, and this process can be reversed to produce stable full-length dimeric gephyrin. Our data suggest a mechanism by which induced conformational transitions of trimeric gephyrin may generate a reversible postsynaptic scaffold for GlyR recruitment, which allows for dynamic receptor movement in and out of postsynaptic GlyR clusters, and thus for synaptic plasticity.


    Organizational Affiliation

    European Molecular Biology Laboratory, Grenoble, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gephyrin
A, B
421Rattus norvegicusMutation(s): 0 
Gene Names: Gphn (Gph)
Find proteins for Q03555 (Rattus norvegicus)
Go to UniProtKB:  Q03555
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
49-mer fragment of Glycine receptor beta chain
P
49Rattus norvegicusMutation(s): 0 
Gene Names: Glrb
Find proteins for P20781 (Rattus norvegicus)
Go to UniProtKB:  P20781
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.243 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 161.547α = 90.00
b = 161.547β = 90.00
c = 126.252γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-27
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Refinement description, Version format compliance