1N7F

Crystal structure of the sixth PDZ domain of GRIP1 in complex with liprin C-terminal peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1074/jbc.M212263200
  • Primary Citation of Related Structures:  

  • 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 t ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AMPA receptor interacting protein GRIP
A, B
97Rattus norvegicusMutation(s): 0 
Gene Names: Grip1
Find proteins for P97879 (Rattus norvegicus)
Go to UniProtKB:  P97879
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
8-mer peptide from interacting protein (liprin)
C, D
8Homo sapiensMutation(s): 0 
Gene Names: PPFIA1 (LIP1)
Find proteins for Q13136 (Homo sapiens)
Go to Gene View: PPFIA1
Go to UniProtKB:  Q13136
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.200 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 117.790α = 90.00
b = 117.790β = 90.00
c = 101.974γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
CCP4data scaling
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-08-12
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance