1FHW

Structure of the pleckstrin homology domain from GRP1 in complex with inositol(1,3,4,5,6)pentakisphosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for discrimination of 3-phosphoinositides by pleckstrin homology domains

Ferguson, K.M.Kavran, J.M.Sankaran, V.G.Fournier, E.Isakoff, S.J.Skolnik, E.Y.Lemmon, M.A.

(2000) Mol.Cell 6: 373-384

  • Primary Citation of Related Structures:  
  • Also Cited By: 1EAZ

  • PubMed Abstract: 
  • Pleckstrin homology (PH) domains are protein modules of around 120 amino acids found in many proteins involved in cellular signaling. Certain PH domains drive signal-dependent membrane recruitment of their host proteins by binding strongly and specif ...

    Pleckstrin homology (PH) domains are protein modules of around 120 amino acids found in many proteins involved in cellular signaling. Certain PH domains drive signal-dependent membrane recruitment of their host proteins by binding strongly and specifically to lipid second messengers produced by agonist-stimulated phosphoinositide 3-kinases (PI 3-Ks). We describe X-ray crystal structures of two different PH domains bound to Ins(1,3,4,5)P4, the head group of the major PI 3-K product PtdIns(3,4,5)P3. One of these PH domains (from Grp1) is PtdIns(3,4,5)P3 specific, while the other (from DAPP1/PHISH) binds strongly to both PtdIns(3,4,5)P3 and its 5'-dephosphorylation product, PtdIns(3,4)P2. Comparison of the two structures provides an explanation for the distinct phosphoinositide specificities of the two PH domains and allows us to predict the 3-phosphoinositide selectivity of uncharacterized PH domains.


    Organizational Affiliation

    Department of Biochemistry and Biophysics and The Johnson Foundation, University of Pennsylvania School of Medicine, Philadelphia 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GUANINE NUCLEOTIDE EXCHANGE FACTOR AND INTEGRIN BINDING PROTEIN HOMOLOG GRP1
A, B
129Mus musculusMutation(s): 0 
Gene Names: Cyth3 (Grp1, Pscd3)
Find proteins for O08967 (Mus musculus)
Go to UniProtKB:  O08967
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
I5P
Query on I5P

Download SDF File 
Download CCD File 
A, B
INOSITOL-(1,3,4,5,6)-PENTAKISPHOSPHATE
C6 H17 O21 P5
CTPQAXVNYGZUAJ-ADOSBGCESA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
I5PKd: 330 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.970α = 90.00
b = 72.220β = 93.21
c = 46.900γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MLPHAREphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-08-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance