1BE9

THE THIRD PDZ DOMAIN FROM THE SYNAPTIC PROTEIN PSD-95 IN COMPLEX WITH A C-TERMINAL PEPTIDE DERIVED FROM CRIPT.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ.

Doyle, D.A.Lee, A.Lewis, J.Kim, E.Sheng, M.MacKinnon, R.

(1996) Cell 85: 1067-1076

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Modular PDZ domains, found in many cell junction-associated proteins, mediate the clustering of membrane ion channels by binding to their C-terminus. The X-ray crystallographic structures of the third PDZ domain from the synaptic protein PSD-95 in co ...

    Modular PDZ domains, found in many cell junction-associated proteins, mediate the clustering of membrane ion channels by binding to their C-terminus. The X-ray crystallographic structures of the third PDZ domain from the synaptic protein PSD-95 in complex with and in the absence of its peptide ligand have been determined at 1.8 angstroms and 2.3 angstroms resolution, respectively. The structures reveal that a four-residue C-terminal stretch (X-Thr/Ser-X-Val-COO(-)) engages the PDZ domain through antiparallel main chain interactions with a beta sheet of the domain. Recognition of the terminal carboxylate group of the peptide is conferred by a cradle of main chain amides provided by a Gly-Leu-Gly-Phe loop as well as by an arginine side chain. Specific side chain interactions and a prominent hydrophobic pocket explain the selective recognition of the C-terminal consensus sequence.


    Related Citations: 
    • Crystal Structure of a Pdz Domain
      Cabral, M.,Petosa, C.,Sutcliffe, M.J.,Raza, S.,Byron, O.,Poy, F.,Marfatia, S.M.,Chishti, A.H.,Liddington, R.C.
      (1996) Nature 382: 649
    • Cript, a Novel Postsynaptic Protein that Binds to the Third Pdz Domain of Psd-95/Sap90
      Niethammer, M.,Valtschanoff, J.G.,Kapoor, T.M.,Allison, D.W.,Weinberg, T.M.,Craig, A.M.,Sheng, M.
      (1998) Neuron 20: 693
    • Crystal Structure of the Hcask Pdz Domain Reveals the Structural Basis of Class II Pdz Domain Target Recognition
      Daniels, D.L.,Cohen, A.R.,Anderson, J.M.,Brunger, A.T.
      (1998) Nat.Struct.Mol.Biol. 5: 317


    Organizational Affiliation

    Laboratory of Molecular Neurobiology and Biophysics, The Rockefeller University, New York, NY 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PSD-95
A
119Rattus norvegicusMutation(s): 0 
Gene Names: Dlg4 (Dlgh4, Psd95)
Find proteins for P31016 (Rattus norvegicus)
Go to UniProtKB:  P31016
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CRIPT
B
5N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.207 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 89.340α = 90.00
b = 89.340β = 90.00
c = 89.340γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORphasing
X-PLORmodel building
MOSFLMdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-21
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-03-07
    Type: Data collection, Other