6QJI

Crystal Structure of the third PDZ domain of PSD-95 protein: space group P3112


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 

  • 5OIB - determined by Camara-Artigas, A.  

Literature

Conformational changes in the third PDZ domain of the neuronal postsynaptic density protein 95.

Camara-Artigas, A.Murciano-Calles, J.Martinez, J.C.

(2019) Acta Crystallogr D Struct Biol 75: 381-391

  • DOI: 10.1107/S2059798319001980
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PDZ domains are protein-protein recognition modules that interact with other proteins through short sequences at the carboxyl terminus. These domains are structurally characterized by a conserved fold composed of six β-strands and two α-helices. The ...

    PDZ domains are protein-protein recognition modules that interact with other proteins through short sequences at the carboxyl terminus. These domains are structurally characterized by a conserved fold composed of six β-strands and two α-helices. The third PDZ domain of the neuronal postsynaptic density protein 95 has an additional α-helix (α3), the role of which is not well known. In previous structures, a succinimide was identified in the β2-β3 loop instead of Asp332. The presence of this modified residue results in conformational changes in α3. In this work, crystallographic structures of the following have been solved: a truncated form of the third PDZ domain of the neuronal postsynaptic density protein 95 from which α3 has been removed, D332P and D332G variants of the protein, and a new crystal form of this domain showing the binding of Asp332 to the carboxylate-binding site of a symmetry-related molecule. Crystals of the wild type and variants were obtained in different space groups, which reflects the conformational plasticity of the domain. Indeed, the overall analysis of these structures suggests that the conformation of the β2-β3 loop is correlated with the fold acquired by α3. The alternate conformation of the β2-β3 loop affects the electrostatics of the carboxylate-binding site and might modulate the binding of different PDZ-binding motifs.


    Organizational Affiliation

    Department of Chemistry and Physics, Agrifood Campus of International Excellence (ceiA3) and CIAMBITAL, University of Almería, Carretera de Sacramento, 04120 Almeria, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Disks large homolog 4
A, B, C, D, E, F
99Homo sapiensMutation(s): 0 
Gene Names: DLG4 (PSD95)
Find proteins for P78352 (Homo sapiens)
Go to Gene View: DLG4
Go to UniProtKB:  P78352
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.212 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 61.970α = 90.00
b = 61.970β = 90.00
c = 228.365γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
Cootmodel building
PHASERphasing
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2019-01-24 
  • Released Date: 2019-04-17 
  • Deposition Author(s): Camara-Artigas, A.
  • This entry supersedes: 5OIB

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBIO2016-78020-R

Revision History 

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-04-24
    Type: Data collection, Database references