1FAO | pdb_00001fao

STRUCTURE OF THE PLECKSTRIN HOMOLOGY DOMAIN FROM DAPP1/PHISH IN COMPLEX WITH INOSITOL 1,3,4,5-TETRAKISPHOSPHATE

• PDB DOI: https://doi.org/10.2210/pdb1FAO/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2000-07-13 Released: 2000-07-20 
• Deposition Author(s): Ferguson, K.M., Kavran, J.M., Sankaran, V.G., Fournier, E., Isakoff, S.J., Skolnik, E.Y., Lemmon, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.232 (Depositor) 
• R-Value Work: 
  0.219 (Depositor) 

Starting Model: experimental

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

• PubMed: 10983984 
• DOI: https://doi.org/10.1016/s1097-2765(00)00037-x
• Primary Citation Related Structures: 
  1FAO, 1FB8, 1FHW, 1FHX


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.31 kDa 
• Atom Count: 971 
• Modeled Residue Count: 100 
• Deposited Residue Count: 126 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUAL ADAPTOR OF PHOSPHOTYROSINE AND 3-PHOSPHOINOSITIDES	A	126	Homo sapiens	Mutation(s): 0  Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UN19 (Homo sapiens) Explore Q9UN19  Go to UniProtKB:  Q9UN19
PHAROS:  Q9UN19 GTEx:  ENSG00000070190

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4IP	B [auth A]	INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE C6 H16 O18 P4 CIPFCGZLFXVXBG-CNWJWELYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.232 (Depositor) 
• R-Value Work:  0.219 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.674	α = 90
b = 46.273	β = 90
c = 64.743	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-07-20 
Deposition Author(s): Ferguson, K.M., Kavran, J.M., Sankaran, V.G., Fournier, E., Isakoff, S.J., Skolnik, E.Y., Lemmon, M.A.

Revision History  

• Version 1.0: 2000-07-20
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary