Crystal structure of the sixth PDZ domain of GRIP1

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 

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Crystal structure of GRIP1 PDZ6-peptide complex reveals the structural basis for class II PDZ target recognition and PDZ domain-mediated multimerization

Im, Y.J.Park, S.H.Rho, S.H.Lee, J.H.Kang, G.B.Sheng, M.Kim, E.Eom, S.H.

(2003) J Biol Chem 278: 8501-8507

  • DOI: https://doi.org/10.1074/jbc.M212263200
  • Primary Citation of Related Structures:  
    1N7E, 1N7F

  • PubMed Abstract: 

    PDZ domains bind to short segments within target proteins in a sequence-specific fashion. Glutamate receptor-interacting protein (GRIP)/ABP family proteins contain six to seven PDZ domains and interact via the sixth PDZ domain (class II) with the C termini of various proteins including liprin-alpha. In addition the PDZ456 domain mediates the formation of homo- and heteromultimers of GRIP proteins. To better understand the structural basis of peptide recognition by a class II PDZ domain and PDZ-mediated multimerization, we determined the crystal structures of the GRIP1 PDZ6 domain alone and in complex with a synthetic C-terminal octapeptide of human liprin-alpha at resolutions of 1.5 and 1.8 A, respectively. Remarkably, unlike other class II PDZ domains, Ile-736 at alphaB5 rather than conserved Leu-732 at alphaB1 makes a direct hydrophobic contact with the side chain of the Tyr at the -2 position of the ligand. Moreover, the peptide-bound structure of PDZ6 shows a slight reorientation of helix alphaB, indicating that the second hydrophobic pocket undergoes a conformational adaptation to accommodate the bulkiness of the Tyr side chain, and forms an antiparallel dimer through an interface located at a site distal to the peptide-binding groove. This configuration may enable formation of GRIP multimers and efficient clustering of GRIP-binding proteins.

  • Organizational Affiliation

    Department of Life Science, Kwangju Institute of Science and Technology, Gwangju 500-712, South Korea.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AMPA receptor interacting protein GRIP97Rattus norvegicusMutation(s): 0 
Gene Names: Grip1
Find proteins for P97879 (Rattus norvegicus)
Explore P97879 
Go to UniProtKB:  P97879
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP97879
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.254 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.267α = 90
b = 40.267β = 90
c = 222.872γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-08-12
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references