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 
  • R-Value Observed: 0.246 

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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
  • Primary Citation of Related Structures:  
    1T3E

  • 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 causes the spontaneous dimerization of its C-terminal region (gephyrin-E), which binds a GlyR beta-subunit-derived peptide with high and low affinity ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GephyrinA, B421Rattus norvegicusMutation(s): 0 
Gene Names: GphnGph
EC: 2.7.7.75 (UniProt), 2.10.1.1 (UniProt)
UniProt
Find proteins for Q03555 (Rattus norvegicus)
Explore Q03555 
Go to UniProtKB:  Q03555
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
49-mer fragment of Glycine receptor beta chainC [auth P]49Rattus norvegicusMutation(s): 0 
Gene Names: Glrb
UniProt
Find proteins for P20781 (Rattus norvegicus)
Explore P20781 
Go to UniProtKB:  P20781
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.246 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.547α = 90
b = 161.547β = 90
c = 126.252γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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