3ZRT

Crystal structure of human PSD-95 PDZ1-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

wwPDB Validation   3D Report Full Report


This is version 1.1 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 U S A 109: 3317

  • DOI: 10.1073/pnas.1113761109
  • Primary Citation of Related Structures:  
    3ZRT

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DISKS LARGE HOMOLOG 4ABCD199Homo sapiensMutation(s): 0 
Gene Names: DLG4PSD95
Find proteins for P78352 (Homo sapiens)
Explore P78352 
Go to UniProtKB:  P78352
NIH Common Fund Data Resources
PHAROS  P78352
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.15α = 90
b = 112.15β = 90
c = 196.13γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Derived calculations, Other