5OVC

PDZ domain from rat Shank3 bound to the C terminus of GKAP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for PDZ domain interactions in the post-synaptic density scaffolding protein Shank3.

Ponna, S.K.Ruskamo, S.Myllykoski, M.Keller, C.Boeckers, T.M.Kursula, P.

(2018) J. Neurochem. 145: 449-463

  • DOI: 10.1111/jnc.14322
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Shank proteins are crucial scaffolding elements of the post-synaptic density (PSD). One of the best-characterized domains in Shank is the PDZ domain, which binds to C-terminal segments of several other PSD proteins. We carried out a detailed stru ...

    The Shank proteins are crucial scaffolding elements of the post-synaptic density (PSD). One of the best-characterized domains in Shank is the PDZ domain, which binds to C-terminal segments of several other PSD proteins. We carried out a detailed structural analysis of Shank3 PDZ domain-peptide complexes, in order to understand determinants of binding affinity towards different ligand proteins. Ligand peptides from four different proteins were cocrystallized with the Shank3 PDZ domain, and binding affinities were determined calorimetrically. In addition, to conserve class I interactions between the first and third C-terminal peptide residue and Shank3, side chain interactions of other residues in the peptide with the PDZ domain are important factors in defining affinity. Structural conservation suggests that the binding specificities of the PDZ domains from different Shanks are similar. Two conserved buried water molecules in PDZ domains may affect correct local folding of ligand recognition determinants. The solution structure of a tandem Shank3 construct containing the SH3 and PDZ domains showed that the two domains are close to each other, which could be of relevance, when recognizing and binding full target proteins. The SH3 domain did not affect the affinity of the PDZ domain towards short target peptides, and the schizophrenia-linked Shank3 mutation R536W in the linker between the domains had no effect on the structure or peptide interactions of the Shank3 SH3-PDZ unit. Our data show the spatial arrangement of two adjacent Shank domains and pinpoint affinity determinants for short PDZ domain ligands with limited sequence homology. This article is protected by copyright. All rights reserved.


    Organizational Affiliation

    Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Finland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SH3 and multiple ankyrin repeat domains protein 3
A
96Rattus norvegicusMutation(s): 0 
Gene Names: Shank3 (Prosap2)
Find proteins for Q9JLU4 (Rattus norvegicus)
Go to UniProtKB:  Q9JLU4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GKAP C terminus, synthetic peptide
B
7Rattus norvegicusMutation(s): 0 
Gene Names: Dlgap1 (Gkap)
Find proteins for P97836 (Rattus norvegicus)
Go to UniProtKB:  P97836
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
B
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.175 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 51.550α = 90.00
b = 51.550β = 90.00
c = 81.770γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-07-11
    Type: Data collection, Database references