2GZV

The cystal structure of the PDZ domain of human PICK1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of PICK1 and other PDZ domains obtained with the help of self-binding C-terminal extensions.

Elkins, J.M.Papagrigoriou, E.Berridge, G.Yang, X.Phillips, C.Gileadi, C.Savitsky, P.Doyle, D.A.

(2007) Protein Sci 16: 683-694

  • DOI: 10.1110/ps.062657507
  • Primary Citation of Related Structures:  
    2IWQ, 2IWP, 2IWO, 2IWN, 2GZV, 2FNE, 2FCF, 2HE4, 2HE2, 2I1N

  • PubMed Abstract: 
  • PDZ domains are protein-protein interaction modules that generally bind to the C termini of their target proteins. The C-terminal four amino acids of a prospective binding partner of a PDZ domain are typically the determinants of binding specificity. ...

    PDZ domains are protein-protein interaction modules that generally bind to the C termini of their target proteins. The C-terminal four amino acids of a prospective binding partner of a PDZ domain are typically the determinants of binding specificity. In an effort to determine the structures of a number of PDZ domains we have included appropriate four residue extensions on the C termini of PDZ domain truncation mutants, designed for self-binding. Multiple truncations of each PDZ domain were generated. The four residue extensions, which represent known specificity sequences of the target PDZ domains and cover both class I and II motifs, form intermolecular contacts in the expected manner for the interactions of PDZ domains with protein C termini for both classes. We present the structures of eight unique PDZ domains crystallized using this approach and focus on four which provide information on selectivity (PICK1 and the third PDZ domain of DLG2), binding site flexibility (the third PDZ domain of MPDZ), and peptide-domain interactions (MPDZ 12th PDZ domain). Analysis of our results shows a clear improvement in the chances of obtaining PDZ domain crystals by using this approach compared to similar truncations of the PDZ domains without the C-terminal four residue extensions.


    Organizational Affiliation

    Structural Genomics Consortium, Oxford University, Botnar Research Centre, Oxford, OX3 7LD, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PRKCA-binding proteinA114Homo sapiensMutation(s): 0 
Gene Names: PICK1PRKCABP
Find proteins for Q9NRD5 (Homo sapiens)
Explore Q9NRD5 
Go to UniProtKB:  Q9NRD5
NIH Common Fund Data Resources
PHAROS  Q9NRD5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.588α = 90
b = 37.257β = 95.75
c = 29.442γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2006-07-18
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description, Structure summary