3L4F

Crystal Structure of betaPIX Coiled-Coil Domain and Shank PDZ Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.272 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for asymmetric association of the betaPIX coiled coil and shank PDZ

Im, Y.J.Kang, G.B.Lee, J.H.Park, K.R.Song, H.E.Kim, E.Song, W.K.Park, D.Eom, S.H.

(2010) J.Mol.Biol. 397: 457-466

  • DOI: 10.1016/j.jmb.2010.01.048

  • PubMed Abstract: 
  • betaPIX (p21-activated kinase interacting exchange factor) and Shank/ProSAP protein form a complex acting as a protein scaffold that integrates signaling pathways and regulates postsynaptic structure. Complex formation is mediated by the C-terminal P ...

    betaPIX (p21-activated kinase interacting exchange factor) and Shank/ProSAP protein form a complex acting as a protein scaffold that integrates signaling pathways and regulates postsynaptic structure. Complex formation is mediated by the C-terminal PDZ binding motif of betaPIX and the Shank PDZ domain. The coiled-coil (CC) domain upstream of the PDZ binding motif allows multimerization of betaPIX, which is important for its physiological functions. We have solved the crystal structure of the betaPIX CC-Shank PDZ complex and determined the stoichiometry of complex formation. The betaPIX CC forms a 76-A-long parallel CC trimer. Despite the fact that the betaPIX CC exposes three PDZ binding motifs in the C-termini, the betaPIX trimer associates with a single Shank PDZ. One of the C-terminal ends of the CC forms an extensive beta-sheet interaction with the Shank PDZ, while the other two ends are not involved in ligand binding and form random coils. The two C-terminal ends of betaPIX have significantly lower affinity than the first PDZ binding motif due to the steric hindrance in the C-terminal tails, which results in binding of a single PDZ domain to the betaPIX trimer. The structure shows canonical class I PDZ binding with a beta-sheet interaction extending to position -6 of betaPIX. The betaB-betaC loop of Shank PDZ undergoes a conformational change upon ligand binding to form the beta-sheet interaction and to accommodate the bulky side chain of Trp -5. This structural study provides a clear picture of the molecular recognition of the PDZ ligand and the asymmetric association of betaPIX CC and Shank PDZ.


    Organizational Affiliation

    College of Pharmacy, Chonnam National University, Gwangju 500-757, South Korea. youngjun.im@gmail.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rho guanine nucleotide exchange factor 7
A, B, C
61Rattus norvegicusMutation(s): 0 
Gene Names: Arhgef7 (Pak3bp, Pixb)
Find proteins for O55043 (Rattus norvegicus)
Go to UniProtKB:  O55043
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SH3 and multiple ankyrin repeat domains protein 1
D
132Rattus norvegicusMutation(s): 0 
Gene Names: Shank1
Find proteins for Q9WV48 (Rattus norvegicus)
Go to UniProtKB:  Q9WV48
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.272 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 47.666α = 90.00
b = 47.666β = 90.00
c = 263.161γ = 120.00
Software Package:
Software NamePurpose
SOLVEphasing
HKL-2000data scaling
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-02-26
    Type: Database references