5C79

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.str.2015.08.008
  • Primary Citation of Related Structures:  
    5C6R, 5C79

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Arf-GAP
A, B
150Mus musculusMutation(s): 0 
Gene Names: Asap1Ddef1Kiaa1249Shag1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QWY8 (Mus musculus)
Explore Q9QWY8 
Go to UniProtKB:  Q9QWY8
IMPC:  MGI:1342335
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QWY8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PBU
Query on PBU

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B],
F [auth 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
C17 H33 O19 P3
DHAFWWKSHUBGAH-BXJBXBQISA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.543α = 90
b = 64.697β = 95.63
c = 44.428γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-10-07
    Type: Initial release
  • Version 1.1: 2015-11-18
    Changes: Database references
  • Version 1.2: 2016-03-16
    Changes: Data collection
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary