1BTN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

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Ligand Structure Quality Assessment 


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

  • Primary Citation of Related Structures:  
    1BTN

  • 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 and soluble inositol phosphates using both circular dichroism and nuclear magnetic resonance spectroscopy, and X-ray crystallography ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-SPECTRINA106Mus musculusMutation(s): 0 
Gene Names: MUSSPNA.GBRODSptbn1ElfSpnb-2Spnb2Sptb2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q62261 (Mus musculus)
Explore Q62261 
Go to UniProtKB:  Q62261
IMPC:  MGI:98388
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I3P (Subject of Investigation/LOI)
Query on I3P

Download Ideal Coordinates CCD File 
B [auth A]D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
C6 H15 O15 P3
MMWCIQZXVOZEGG-XJTPDSDZSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
I3P Binding MOAD:  1BTN Kd: 4.00e+4 (nM) from 1 assay(s)
PDBBind:  1BTN Kd: 4.00e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: P 4 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69α = 90
b = 69β = 90
c = 50.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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