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 3ZRT | pdb_00003zrt

Crystal structure of human PSD-95 PDZ1-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.264 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.219 (Depositor) 
  • R-Value Observed: 
    0.221 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 3ZRT

This is version 1.2 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: https://doi.org/10.1073/pnas.1113761109
  • Primary Citation 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 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

Macromolecule Content 

  • Total Structure Weight: 85.39 kDa 
  • Atom Count: 5,311 
  • Modeled Residue Count: 704 
  • Deposited Residue Count: 796 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DISKS LARGE HOMOLOG 4
A, B, C, D
199Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P78352 (Homo sapiens)
Explore P78352 
Go to UniProtKB:  P78352
PHAROS:  P78352
GTEx:  ENSG00000132535 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78352
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.264 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.219 (Depositor) 
  • R-Value Observed: 0.221 (Depositor) 
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  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Derived calculations, Other
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Refinement description