6SPZ

Crystal structure of PDZ1-2 from PSD-95 with peptide ligand sequence RRESEI bound to both domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The Dual PDZ Domain from Postsynaptic Density Protein 95 Forms a Scaffold with Peptide Ligand.

Rodzli, N.A.Lockhart-Cairns, M.P.Levy, C.W.Chipperfield, J.Bird, L.Baldock, C.Prince, S.M.

(2020) Biophys J 119: 667-689

  • DOI: https://doi.org/10.1016/j.bpj.2020.06.018
  • Primary Citation of Related Structures:  
    6SPV, 6SPZ

  • PubMed Abstract: 

    PSD-95 is a member of the membrane-associated guanylate kinase class of proteins that forms scaffolding interactions with partner proteins, including ion and receptor channels. PSD-95 is directly implicated in modulating the electrical responses of excitable cells. The first two PSD-95/disks large/zona occludens (PDZ) domains of PSD-95 have been shown to be the key component in the formation of channel clusters. We report crystal structures of this dual domain in both apo- and ligand-bound form: thermodynamic analysis of the ligand association and small-angle x-ray scattering of the dual domain in the absence and presence of ligands. These experiments reveal that the ligated double domain forms a three-dimensional scaffold that can be described by a space group. The concentration of the components in this study is comparable with those found in compartments of excitable cells such as the postsynaptic density and juxtaparanodes of Ranvier. These in vitro experiments inform the basis of the scaffolding function of PSD-95 and provide a detailed model for scaffold formation by the PDZ domains of PSD-95.


  • Organizational Affiliation

    Wellcome Centre for Cell-Matrix Research, Division of Cell-Matrix Biology and Regenerative Medicine, Manchester Academic Health Science Centre, Manchester, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Disks large homolog 4197Homo sapiensMutation(s): 0 
Gene Names: DLG4PSD95
UniProt & NIH Common Fund Data Resources
Find proteins for P78352 (Homo sapiens)
Explore P78352 
Go to UniProtKB:  P78352
GTEx:  ENSG00000132535 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78352
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ARG-ARG-GLU-SER-GLU-ILEB [auth P],
C [auth Q]
6Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P63252 (Homo sapiens)
Explore P63252 
Go to UniProtKB:  P63252
GTEx:  ENSG00000123700 
Entity Groups  
UniProt GroupP63252
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSH (Subject of Investigation/LOI)
Query on GSH

Download Ideal Coordinates CCD File 
D [auth A]GLUTATHIONE
C10 H17 N3 O6 S
RWSXRVCMGQZWBV-WDSKDSINSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.200 
  • Space Group: I 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.5α = 90
b = 50.5β = 90
c = 176.37γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
XDSdata reduction
SCALAdata scaling
pointlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-02
    Type: Initial release
  • Version 1.1: 2020-07-22
    Changes: Database references
  • Version 1.2: 2020-08-19
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description