5C6R | pdb_00005c6r

Crystal structure of PH domain of ASAP1

• PDB DOI: https://doi.org/10.2210/pdb5C6R/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-06-23 Released: 2015-10-07 
• Deposition Author(s): Xia, D., Tang, W.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.260 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.214 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

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

• PubMed: 26365802 
• DOI: https://doi.org/10.1016/j.str.2015.08.008
• Primary Citation 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.

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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.
Laboratory of Structural Biophysics, National Heart, Lung and Blood 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 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: [e-mail].
Laboratory of Cellular and Molecular Biology, National Cancer Institute, National Institutes of Health, Building 37, Room 2042, Bethesda, MD 20892, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 35.15 kDa 
• Atom Count: 1,838 
• Modeled Residue Count: 218 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arf-GAP	A, B	150	Mus musculus	Mutation(s): 0  Gene Names: Asap1, Ddef1, Kiaa1249, Shag1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9QWY8 (Mus musculus) Explore Q9QWY8  Go to UniProtKB:  Q9QWY8
IMPC:  MGI:1342335

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	D [auth A], E [auth A], F [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4	C [auth A], G [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.260 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.214 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.12	α = 90
b = 48.12	β = 90
c = 111.333	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description