5C4G: Crystal Structure Of An Engineered Construct Of Phosphatidylinositol 4 Kinase Iii Beta With The Inhibitor Bqr695 In Complex With Gdp Loaded Rab11

The ability of proteins to bind and interact with protein partners plays fundamental roles in many cellular contexts. X-ray crystallography has been a powerful approach to understand protein-protein interactions; however, a challenge in the crystallization of proteins and their complexes is the presence of intrinsically disordered regions. In this article, we describe an application of hydrogen deuterium exchange mass spectrometry (HDX-MS) to identify dynamic regions within type III phosphatidylinositol 4 kinase beta (PI4KIIIbeta) in complex with the GTPase Rab11. This information was then used to design deletions that allowed for the production of diffraction quality crystals. Importantly, we also used HDX-MS to verify that the new construct was properly folded, consistent with it being catalytically and functionally active. Structures of PI4KIIIbeta in an Apo state and bound to the potent inhibitor BQR695 in complex with both GTPgammaS and GDP loaded Rab11 were determined. This hybrid HDX-MS/crystallographic strategy revealed novel aspects of the PI4KIIIbeta-Rab11 complex, as well as the molecular mechanism of potency of a PI4K specific inhibitor (BQR695). This approach is widely applicable to protein-protein complexes, and is an excellent strategy to optimize constructs for high-resolution structural approaches.
PDB ID: 5C4GDownload
MMDB ID: 135713
PDB Deposition Date: 2015/6/18
Updated in MMDB: 2017/10
Experimental Method:
x-ray diffraction
Resolution: 3.2  Å
Source Organism:
Similar Structures:
Biological Unit for 5C4G: dimeric; determined by author and by software (PISA)
Molecular Components in 5C4G
Label Count Molecule
Proteins (2 molecules)
Ras-related Protein Rab-11a(Gene symbol: RAB11A)
Molecule annotation
Phosphatidylinositol 4-kinase Beta(Gene symbol: PI4KB)
Molecule annotation
Chemicals (5 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB