1BTN

STRUCTURE OF THE BINDING SITE FOR INOSITOL PHOSPHATES IN A PH DOMAIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.205 

wwPDB Validation  3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the binding site for inositol phosphates in a PH domain.

Hyvonen, M.Macias, M.J.Nilges, M.Oschkinat, H.Saraste, M.Wilmanns, M.

(1995) EMBO J. 14: 4676-4685


  • PubMed Abstract: 
  • Phosphatidylinositol bisphosphate has been found to bind specifically to pleckstrin homology (PH) domains that are commonly present in signalling proteins but also found in cytoskeleton. We have studied the complexes of the beta-spectrin PH domain an ...

    Phosphatidylinositol bisphosphate has been found to bind specifically to pleckstrin homology (PH) domains that are commonly present in signalling proteins but also found in cytoskeleton. We have studied the complexes of the beta-spectrin PH domain and soluble inositol phosphates using both circular dichroism and nuclear magnetic resonance spectroscopy, and X-ray crystallography. The specific binding site is located in the centre of a positively charged surface patch of the domain. The presence of 4,5-bisphosphate group on the inositol ring is critical for binding. In the crystal structure that has been determined at 2.0 A resolution, inositol-1,4,5-trisphosphate is bound with salt bridges and hydrogen bonds through these phosphate groups whereas the 1-phosphate group is mostly solvent-exposed and the inositol ring has virtually no interactions with the protein. We propose a model in which PH domains are involved in reversible anchoring of proteins to membranes via their specific binding to phosphoinositides. They could also participate in a response to a second messenger such as inositol trisphosphate, organizing cross-roads in cellular signalling.


    Related Citations: 
    • Structure of the Ph Domain from Beta-Spectrin
      Macias, M.J.,Musacchio, A.,Postingl, H.,Nilges, M.,Saraste, M.,Oschkinat, H.
      (1994) Nature 369: 675


    Organizational Affiliation

    European Molecular Biology Laboratory, Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule Chains Sequence Length Organism Details
BETA-SPECTRIN
A
106 Mus musculus Gene Names: Sptbn1 (Elf, Spnb-2, Spnb2, Sptb2)
Find proteins for Q62261 (Mus musculus)
Go to UniProtKB:  Q62261
Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
I3P
Query on I3P

Download SDF File 
Download CCD File 
A
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
C6 H15 O15 P3
MMWCIQZXVOZEGG-XJTPDSDZSA-N
 Ligand Interaction
External Ligand Annotations 
ID Binding Affinity (Sequence Identity %)
I3P Kd: 40000 nM BINDINGMOAD
I3P Kd: 40000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.205 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å) Angle (°)
a = 69.000 α = 90.00
b = 69.000 β = 90.00
c = 50.800 γ = 90.00
Software Package:
Software Name Purpose
XDS data reduction
X-PLOR model building
X-PLOR refinement
X-PLOR phasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance