Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D4  (3D View)
Global Stoichiometry: Homo 16-mer - A16 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 88.50 kDa 
• Atom Count: 5724 
• Modelled Residue Count: 694 
• Deposited Residue Count: 768 
• Unique protein chains: 1

4HNE

Crystal structure of the catalytic domain of human type II alpha Phosphatidylinositol 4-kinase (PI4KIIalpha) in complex with ADP

• DOI: 10.2210/pdb4HNE/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-10-19 Released: 2014-04-09 
• Deposition Author(s): Zhou, Q., Zhai, Y., Zhang, K., Chen, C., Sun, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.251 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Literature

Molecular insights into the membrane-associated phosphatidylinositol 4-kinase II alpha.

Zhou, Q., Li, J., Yu, H., Zhai, Y., Gao, Z., Liu, Y., Pang, X., Zhang, L., Schulten, K., Sun, F., Chen, C.

(2014) Nat Commun 5: 3552-3552

• PubMed: 24675427 
• DOI: 10.1038/ncomms4552
• Primary Citation of Related Structures:  
  4HND, 4HNE


• PubMed Abstract: 
  

Phosphatidylinositol 4-kinase IIα (PI4KIIα), a membrane-associated PI kinase, plays a central role in cell signalling and trafficking. Its kinase activity critically depends on palmitoylation of its cysteine-rich motif (-CCPCC-) and is modulated by the membrane environment. Lack of atomic structure impairs our understanding of the mechanism regulating kinase activity. Here we present the crystal structure of human PI4KIIα in ADP-bound form. The structure identifies the nucleotide-binding pocket that differs notably from that found in PI3Ks. Two structural insertions, a palmitoylation insertion and an RK-rich insertion, endow PI4KIIα with the 'integral' membrane-binding feature. Molecular dynamics simulations, biochemical and mutagenesis studies reveal that the palmitoylation insertion, containing an amphipathic helix, contributes to the PI-binding pocket and anchors PI4KIIα to the membrane, suggesting that fluctuation of the palmitoylation insertion affects PI4KIIα's activity. We conclude from our results that PI4KIIα's activity is regulated indirectly through changes in the membrane environment.

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Organizational Affiliation: 

1] National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China [2] Beijing Institute for Brain Disorders, Beijing 100069, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4-kinase type 2-alpha	A, B	384	Homo sapiens	Mutation(s): 4  Gene Names: PI4K2A, PI4KIIA (AMINO ACIDS 78-453) EC: 2.7.1.67
Find proteins for Q9BTU6 (Homo sapiens) Explore Q9BTU6  Go to UniProtKB:  Q9BTU6
NIH Common Fund Data Resources
PHAROS:  Q9BTU6 GTEx:  ENSG00000155252

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	C [auth A], D [auth B]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
ADP	Ki:  100100   nM  BindingDB
ADP	IC50:  145300   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.95 Å
• R-Value Free: 0.251 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 191.824	α = 90
b = 191.824	β = 90
c = 157.543	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-19 
• Released Date: 2014-04-09 
Deposition Author(s): Zhou, Q., Zhai, Y., Zhang, K., Chen, C., Sun, F.

Revision History  

• Version 1.0: 2014-04-09
  Type: Initial release