3ZRT

Crystal structure of human PSD-95 PDZ1-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.398 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A High-Affinity, Dimeric Inhibitor of Psd-95 Bivalently Interacts with Pdz1-2 and Protects Against Ischemic Brain Damage.

Bach, A.Clausen, B.H.Moller, M.Vestergaard, B.Chi, C.N.Round, A.Sorensen, P.L.Nissen, K.B.Kastrup, J.S.Gajhede, M.Jemth, P.Kristensen, A.S.Lundstrom, P.Lambertsen, K.L.Stromgaard, K.

(2012) Proc.Natl.Acad.Sci.USA 109: 3317

  • DOI: 10.1073/pnas.1113761109

  • PubMed Abstract: 
  • Inhibition of the ternary protein complex of the synaptic scaffolding protein postsynaptic density protein-95 (PSD-95), neuronal nitric oxide synthase (nNOS), and the N-methyl-D-aspartate (NMDA) receptor is a potential strategy for treating ischemic ...

    Inhibition of the ternary protein complex of the synaptic scaffolding protein postsynaptic density protein-95 (PSD-95), neuronal nitric oxide synthase (nNOS), and the N-methyl-D-aspartate (NMDA) receptor is a potential strategy for treating ischemic brain damage, but high-affinity inhibitors are lacking. Here we report the design and synthesis of a novel dimeric inhibitor, Tat-NPEG4(IETDV)(2) (Tat-N-dimer), which binds the tandem PDZ1-2 domain of PSD-95 with an unprecedented high affinity of 4.6 nM, and displays extensive protease-resistance as evaluated in vitro by stability-measurements in human blood plasma. X-ray crystallography, NMR, and small-angle X-ray scattering (SAXS) deduced a true bivalent interaction between dimeric inhibitor and PDZ1-2, and also provided a dynamic model of the conformational changes of PDZ1-2 induced by the dimeric inhibitor. A single intravenous injection of Tat-N-dimer (3 nmol/g) to mice subjected to focal cerebral ischemia reduces infarct volume with 40% and restores motor functions. Thus, Tat-N-dimer is a highly efficacious neuroprotective agent with therapeutic potential in stroke.


    Organizational Affiliation

    Department of Medicinal Chemistry, University of Copenhagen, DK-2100 Copenhagen, Denmark. anba@farma.ku.dk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DISKS LARGE HOMOLOG 4
A, B, C, D
199Homo sapiensMutation(s): 0 
Gene Names: DLG4 (PSD95)
Find proteins for P78352 (Homo sapiens)
Go to Gene View: DLG4
Go to UniProtKB:  P78352
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.398 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 112.150α = 90.00
b = 112.150β = 90.00
c = 196.130γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release