4MT6 | pdb_00004mt6

Crystal structure of closed inactive collybistin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å
  • R-Value Free: 
    0.282 (Depositor), 0.296 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4MT6

This is version 1.2 of the entry. See complete history

Literature

A conformational switch in collybistin determines the differentiation of inhibitory postsynapses.

Soykan, T.Schneeberger, D.Tria, G.Buechner, C.Bader, N.Svergun, D.Tessmer, I.Poulopoulos, A.Papadopoulos, T.Varoqueaux, F.Schindelin, H.Brose, N.

(2014) EMBO J 33: 2113-2133

  • DOI: https://doi.org/10.15252/embj.201488143
  • Primary Citation Related Structures: 
    4MT6, 4MT7

  • PubMed Abstract: 

    The formation of neuronal synapses and the dynamic regulation of their efficacy depend on the assembly of the postsynaptic neurotransmitter receptor apparatus. Receptor recruitment to inhibitory GABAergic and glycinergic synapses is controlled by the scaffold protein gephyrin and the adaptor protein collybistin. We derived new insights into the structure of collybistin and used these to design biochemical, cell biological, and genetic analyses of collybistin function. Our data define a collybistin-based protein interaction network that controls the gephyrin content of inhibitory postsynapses. Within this network, collybistin can adopt open/active and closed/inactive conformations to act as a switchable adaptor that links gephyrin to plasma membrane phosphoinositides. This function of collybistin is regulated by binding of the adhesion protein neuroligin-2, which stabilizes the open/active conformation of collybistin at the postsynaptic plasma membrane by competing with an intramolecular interaction in collybistin that favors the closed/inactive conformation. By linking trans-synaptic neuroligin-dependent adhesion and phosphoinositide signaling with gephyrin recruitment, the collybistin-based regulatory switch mechanism represents an integrating regulatory node in the formation and function of inhibitory postsynapses.


  • Organizational Affiliation
    • Department of Molecular Neurobiology, Max Planck Institute of Experimental Medicine, Göttingen, Germany.

Macromolecule Content 

  • Total Structure Weight: 54.08 kDa 
  • Atom Count: 3,298 
  • Modeled Residue Count: 389 
  • Deposited Residue Count: 456 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rho guanine nucleotide exchange factor 9456Rattus norvegicusMutation(s): 2 
Gene Names: Arhgef9
UniProt
Find proteins for Q9QX73 (Rattus norvegicus)
Explore Q9QX73 
Go to UniProtKB:  Q9QX73
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QX73
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å
  • R-Value Free:  0.282 (Depositor), 0.296 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.255 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 217.259α = 90
b = 217.259β = 90
c = 217.259γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
DNAdata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-10-01
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references