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

  • DOI: 10.1016/s0092-8674(00)81307-0
  • Primary Citation of Related Structures:  
    1BE9, 1BFE

  • 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 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 Biol 5: 317
    • 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 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PSD-95A119Rattus norvegicusMutation(s): 0 
Gene Names: Dlg4Dlgh4Psd95
Find proteins for P31016 (Rattus norvegicus)
Explore P31016 
Go to UniProtKB:  P31016
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CRIPTB5N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
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 = 89.34α = 90
b = 89.34β = 90
c = 89.34γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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