2AWW

Synapse associated protein 97 PDZ2 domain variant C378G with C-terminal GluR-A peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Crystal structure of the second PDZ domain of SAP97 in complex with a GluR-A C-terminal peptide

von Ossowski, I., Oksanen, E., von Ossowski, L., Cai, C., Sundberg, M., Goldman, A., Keinanen, K.

(2006) Febs J. 273: 5219-5229

  • DOI: 10.1111/j.1742-4658.2006.05521.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Synaptic targeting of GluR-A subunit-containing glutamate receptors involves an interaction with synapse-associated protein 97 (SAP97). The C-terminus of GluR-A, which contains a class I PDZ ligand motif (-x-Ser/Thr-x-phi-COOH where phi is an aliphat ...

    Synaptic targeting of GluR-A subunit-containing glutamate receptors involves an interaction with synapse-associated protein 97 (SAP97). The C-terminus of GluR-A, which contains a class I PDZ ligand motif (-x-Ser/Thr-x-phi-COOH where phi is an aliphatic amino acid) associates preferentially with the second PDZ domain of SAP97 (SAP97(PDZ2)). To understand the structural basis of this interaction, we have determined the crystal structures of wild-type and a SAP97(PDZ2) variant in complex with an 18-mer C-terminal peptide (residues 890-907) of GluR-A and of two variant PDZ2 domains in unliganded state at 1.8-2.44 A resolutions. SAP97(PDZ2) folds to a compact globular domain comprising six beta-strands and two alpha-helices, a typical architecture for PDZ domains. In the structure of the peptide complex, only the last four C-terminal residues of the GluR-A are visible, and align as an antiparallel beta-strand in the binding groove of SAP97(PDZ2). The free carboxylate group and the aliphatic side chain of the C-terminal leucine (Leu907), and the hydroxyl group of Thr905 of the GluR-A peptide are engaged in essential class I PDZ interactions. Comparison between the free and complexed structures reveals conformational changes which take place upon peptide binding. The betaAlpha-betaBeta loop moves away from the C-terminal end of alphaB leading to a slight opening of the binding groove, which may better accommodate the peptide ligand. The two conformational states are stabilized by alternative hydrogen bond and coulombic interactions of Lys324 in betaAlpha-betaBeta loop with Asp396 or Thr394 in betaBeta. Results of in vitro binding and immunoprecipitation experiments using a PDZ motif-destroying L907A mutation as well as the insertion of an extra alanine residue between the C-terminal Leu907 and the stop codon are also consistent with a 'classical' type I PDZ interaction between SAP97 and GluR-A C-terminus.

    Organizational Affiliation: 

    Department of Biological and Environmental Sciences (Division of Biochemistry), University of Helsinki, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Synapse associated protein 97
A, B
105Rattus norvegicusMutation(s): 1 
Gene Names: Dlg1 (Dlgh1)
Find proteins for Q62696 (Rattus norvegicus)
Go to UniProtKB:  Q62696
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
18-residue C-terminal peptide from glutamate receptor, ionotropic, AMPA1
C
18Rattus norvegicusMutation(s): 0 
Gene Names: Gria1 (Glur1)
Find proteins for P19490 (Rattus norvegicus)
Go to UniProtKB:  P19490
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 34.350α = 90.00
b = 54.310β = 84.03
c = 54.640γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
ProDCdata collection
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description