4U90

GephE in complex with PEG crosslinked GABA receptor alpha3 subunit derived dimeric peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Design and Synthesis of High-Affinity Dimeric Inhibitors Targeting the Interactions between Gephyrin and Inhibitory Neurotransmitter Receptors.

Maric, H.M.Kasaragod, V.B.Haugaard-Kedstrom, L.Hausrat, T.J.Kneussel, M.Schindelin, H.Strmgaard, K.

(2015) Angew.Chem.Int.Ed.Engl. 54: 490-494

  • DOI: 10.1002/anie.201409043
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Gephyrin is the central scaffolding protein for inhibitory neurotransmitter receptors in the brain. Here we describe the development of dimeric peptides that inhibit the interaction between gephyrin and these receptors, a process which is fundamental ...

    Gephyrin is the central scaffolding protein for inhibitory neurotransmitter receptors in the brain. Here we describe the development of dimeric peptides that inhibit the interaction between gephyrin and these receptors, a process which is fundamental to numerous synaptic functions and diseases of the brain. We first identified receptor-derived minimal gephyrin-binding peptides that displayed exclusive binding towards native gephyrin from brain lysates. We then designed and synthesized a series of dimeric ligands, which led to a remarkable 1220-fold enhancement of the gephyrin affinity (KD=6.8 nM). In X-ray crystal structures we visualized the simultaneous dimer-to-dimer binding in atomic detail, revealing compound-specific binding modes. Thus, we defined the molecular basis of the affinity-enhancing effect of multivalent gephyrin inhibitors and provide conceptually novel compounds with therapeutic potential, which will allow further elucidation of the gephyrin-receptor interplay.


    Organizational Affiliation

    Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen (Denmark).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gephyrin
A
419Rattus norvegicusMutation(s): 0 
Gene Names: Gphn (Gph)
Find proteins for Q03555 (Rattus norvegicus)
Go to UniProtKB:  Q03555
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Gamma-aminobutyric acid receptor subunit alpha-3
D, E
10Rattus norvegicusMutation(s): 0 
Gene Names: Gabra3 (Gabra-3)
Find proteins for P20236 (Rattus norvegicus)
Go to UniProtKB:  P20236
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BU1
Query on BU1

Download SDF File 
Download CCD File 
A
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
3F8
Query on 3F8

Download SDF File 
Download CCD File 
E
1,1'-[ethane-1,2-diylbis(oxyethane-2,1-diyl)]bis(1H-pyrrole-2,5-dione)
C14 H16 N2 O6
FERLGYOHRKHQJP-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.167 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 88.538α = 90.00
b = 99.240β = 90.00
c = 114.406γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DFGGermanySchi 425/ 8-1

Revision History 

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-02-11
    Type: Database references