2HE4

The crystal structure of the second PDZ domain of human NHERF-2 (SLC9A3R2) interacting with a mode 1 PDZ binding motif

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 

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This is version 1.2 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, 2FCF, 2FNE, 2BYG, 2GZV, 2HE4, 2HE2

  • 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. In ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Na(+)/H(+) exchange regulatory cofactor NHE-RF2 A90Homo sapiensMutation(s): 1 
Gene Names: SLC9A3R2, NHERF2
Find proteins for Q15599 (Homo sapiens)
Explore Q15599 
Go to UniProtKB:  Q15599
NIH Common Fund Data Resources
PHAROS:  Q15599
GTEx:  ENSG00000065054
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download Ideal Coordinates CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.130 
  • R-Value Observed: 0.132 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.803α = 90
b = 37.677β = 97.7
c = 40.34γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

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: Version format compliance