5C79

PH domain of ASAP1 in complex with diC4-PtdIns(4,5)P2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Basis for Cooperative Binding of Anionic Phospholipids to the PH Domain of the Arf GAP ASAP1.

Jian, X.Tang, W.K.Zhai, P.Roy, N.S.Luo, R.Gruschus, J.M.Yohe, M.E.Chen, P.W.Li, Y.Byrd, R.A.Xia, D.Randazzo, P.A.

(2015) Structure 23: 1977-1988

  • DOI: 10.1016/j.str.2015.08.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We have defined the molecular basis for association of the PH domain of the Arf GAP ASAP1 with phospholipid bilayers. Structures of the unliganded and dibutyryl PtdIns(4,5)P2-bound PH domain were solved. PtdIns(4,5)P2 made contact with both a canonic ...

    We have defined the molecular basis for association of the PH domain of the Arf GAP ASAP1 with phospholipid bilayers. Structures of the unliganded and dibutyryl PtdIns(4,5)P2-bound PH domain were solved. PtdIns(4,5)P2 made contact with both a canonical site (C site) and an atypical site (A site). We hypothesized cooperative binding of PtdIns(4,5)P2 to the C site and a nonspecific anionic phospholipid to the A site. PtdIns(4,5)P2 dependence of binding to large unilamellar vesicles and GAP activity was sigmoidal, consistent with cooperative sites. In contrast, PtdIns(4,5)P2 binding to the PH domain of PLC δ1 was hyperbolic. Mutation of amino acids in either the C or A site resulted in decreased PtdIns(4,5)P2-dependent binding to vesicles and decreased GAP activity. The results support the idea of cooperative phospholipid binding to the C and A sites of the PH domain of ASAP1. We propose that the mechanism underlies rapid switching between active and inactive ASAP1.


    Organizational Affiliation

    Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Structural Biophysics Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Building 37, Room 2042, Bethesda, MD 20892, USA. Electronic address: randazzp@mail.nih.gov.,Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; Laboratory of Cell Biology, National Cancer Institute, Building 37, Room 2122, Bethesda, MD 20892, USA. Electronic address: dixia@helix.nih.gov.,Laboratory of Structural Biophysics, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arf-GAP
A, B
150Mus musculusMutation(s): 0 
Gene Names: Asap1 (Ddef1, Kiaa1249, Shag1)
Find proteins for Q9QWY8 (Mus musculus)
Go to UniProtKB:  Q9QWY8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
PBU
Query on PBU

Download SDF File 
Download CCD File 
A, B
(2R)-3-{[(R)-HYDROXY{[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIHYDROXY-4,5-BIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1,2-DIYL DIBUTANOATE
di-butanoyl L-alpha-phosphatidyl-D-myo-inositol 4,5-bisphosphate; di-C4-PIP2
C17 H33 O19 P3
DHAFWWKSHUBGAH-BXJBXBQISA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PBUKd: 7000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 37.543α = 90.00
b = 64.697β = 95.63
c = 44.428γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-06-24 
  • Released Date: 2015-10-07 
  • Deposition Author(s): Xia, D., Tang, W.K.

Revision History 

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-11-18
    Type: Database references
  • Version 1.2: 2016-03-16
    Type: Data collection