1U29

Triglycine variant of the ARNO Pleckstrin Homology Domain in complex with Ins(1,4,5)P3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural determinants of phosphoinositide selectivity in splice variants of Grp1 family PH domains

Cronin, T.C.DiNitto, J.P.Czech, M.P.Lambright, D.G.

(2004) EMBO J 23: 3711-3720

  • DOI: https://doi.org/10.1038/sj.emboj.7600388
  • Primary Citation of Related Structures:  
    1U27, 1U29, 1U2B

  • PubMed Abstract: 

    The pleckstrin homology (PH) domains of the homologous proteins Grp1 (general receptor for phosphoinositides), ARNO (Arf nucleotide binding site opener), and Cytohesin-1 bind phosphatidylinositol (PtdIns) 3,4,5-trisphosphate with unusually high selectivity. Remarkably, splice variants that differ only by the insertion of a single glycine residue in the beta1/beta2 loop exhibit dual specificity for PtdIns(3,4,5)P(3) and PtdIns(4,5)P(2). The structural basis for this dramatic specificity switch is not apparent from the known modes of phosphoinositide recognition. Here, we report crystal structures for dual specificity variants of the Grp1 and ARNO PH domains in either the unliganded form or in complex with the head groups of PtdIns(4,5)P(2) and PtdIns(3,4,5)P(3). Loss of contacts with the beta1/beta2 loop with no significant change in head group orientation accounts for the significant decrease in PtdIns(3,4,5)P(3) affinity observed for the dual specificity variants. Conversely, a small increase rather than decrease in affinity for PtdIns(4,5)P(2) is explained by a novel binding mode, in which the glycine insertion alleviates unfavorable interactions with the beta1/beta2 loop. These observations are supported by a systematic mutational analysis of the determinants of phosphoinositide recognition.


  • Organizational Affiliation

    Program in Molecular Medicine and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytohesin 2129Mus musculusMutation(s): 0 
Gene Names: Pscd2Sec7b
UniProt
Find proteins for P63034 (Mus musculus)
Explore P63034 
Go to UniProtKB:  P63034
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63034
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I3P
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.998α = 90
b = 56.378β = 90
c = 57.091γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description