6BTZ

Crystal structure of the PI3KC2alpha C2 domain in space group C121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular Basis for Membrane Recruitment by the PX and C2 Domains of Class II Phosphoinositide 3-Kinase-C2 alpha.

Chen, K.E.Tillu, V.A.Chandra, M.Collins, B.M.

(2018) Structure 26: 1612

  • DOI: 10.1016/j.str.2018.08.010
  • Primary Citation of Related Structures:  
    6BUB, 6BTY, 6BTZ, 6BU0

  • PubMed Abstract: 
  • Phosphorylation of phosphoinositides by the class II phosphatidylinositol 3-kinase (PI3K) PI3K-C2α is essential for many processes, including neuroexocytosis and formation of clathrin-coated vesicles. A defining feature of the class II PI3Ks is a C-terminal module composed of phox-homology (PX) and C2 membrane interacting domains; however, the mechanisms that control their specific cellular localization remain poorly understood ...

    Phosphorylation of phosphoinositides by the class II phosphatidylinositol 3-kinase (PI3K) PI3K-C2α is essential for many processes, including neuroexocytosis and formation of clathrin-coated vesicles. A defining feature of the class II PI3Ks is a C-terminal module composed of phox-homology (PX) and C2 membrane interacting domains; however, the mechanisms that control their specific cellular localization remain poorly understood. Here we report the crystal structure of the C2 domain of PI3K-C2α in complex with the phosphoinositide head-group mimic inositol hexaphosphate, revealing two distinct pockets for membrane binding. The C2 domain preferentially binds to phosphatidylinositol 4,5-bisphosphate and phosphatidylinositol (3,4,5)-trisphosphate, and low-resolution structures of the combined PX-C2 module by small-angle X-ray scattering reveal a compact conformation in which cooperative lipid binding by each domain binding can occur. Finally, we demonstrate an unexpected role for calcium in perturbing the membrane interactions of the PX-C2 module, which we speculate may be important for regulating the activity of PI3K-C2α.


    Organizational Affiliation

    Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia. Electronic address: b.collins@imb.uq.edu.au.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 4-phosphate 3-kinase C2 domain-containing subunit alphaA, B, C, D131Homo sapiensMutation(s): 0 
Gene Names: PIK3C2A
EC: 2.7.1.154
UniProt & NIH Common Fund Data Resources
Find proteins for O00443 (Homo sapiens)
Explore O00443 
Go to UniProtKB:  O00443
PHAROS:  O00443
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O4B
Query on O4B

Download Ideal Coordinates CCD File 
BA [auth C], FA [auth D], GA [auth D], I [auth A], J [auth A], S [auth B]1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE
C12 H24 O6
XEZNGIUYQVAUSS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth C] , DA [auth D] , E [auth A] , EA [auth D] , F [auth A] , G [auth A] , H [auth A] , N [auth B] , 
AA [auth C],  DA [auth D],  E [auth A],  EA [auth D],  F [auth A],  G [auth A],  H [auth A],  N [auth B],  O [auth B],  P [auth B],  Q [auth B],  R [auth B],  W [auth C],  X [auth C],  Y [auth C],  Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth C], K [auth A], L [auth A], M [auth A], T [auth B], U [auth B], V [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.346α = 90
b = 61.546β = 92.58
c = 90.496γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-17
    Type: Initial release
  • Version 1.1: 2018-12-19
    Changes: Data collection, Database references