5C4G

Crystal structure of an engineered construct of phosphatidylinositol 4 kinase III beta with the inhibitor BQR695 in complex with GDP loaded Rab11

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 


Literature

Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIII beta with Rab11.

Fowler, M.L., McPhail, J.A., Jenkins, M.L., Masson, G.R., Rutaganira, F.U., Shokat, K.M., Williams, R.L., Burke, J.E.

(2016) Protein Sci 25: 826-839

  • DOI: https://doi.org/10.1002/pro.2879
  • Primary Citation of Related Structures:  
    5C46, 5C4G

  • PubMed Abstract: 

    • 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 ...

    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 (PI4KIIIβ) 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 PI4KIIIβ in an Apo state and bound to the potent inhibitor BQR695 in complex with both GTPγS and GDP loaded Rab11 were determined. This hybrid HDX-MS/crystallographic strategy revealed novel aspects of the PI4KIIIβ-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.

    Organizational Affiliation: 

    Department of Biochemistry and Microbiology, University of Victoria, British Columbia, V8P 5C2, Canada.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rab-11AA [auth B]219Homo sapiensMutation(s): 1 
Gene Names: RAB11A, RAB11
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P62491 (Homo sapiens)
Explore P62491 
Go to UniProtKB:  P62491
PHAROS:  P62491
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62491
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Phosphatidylinositol 4-kinase betaB [auth E]529Homo sapiensMutation(s): 1 
Gene Names: PI4KB, PIK4CB
EC: 2.7.1.67
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBF8 (Homo sapiens)
Explore Q9UBF8 
Go to UniProtKB:  Q9UBF8
PHAROS:  Q9UBF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBF8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
D [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
BQR
Query on BQR
Download Ideal Coordinates CCD File 
G [auth E]N~2~-[7-(3,4-dimethoxyphenyl)quinoxalin-2-yl]-N-methylglycinamide
C19 H20 N4 O3
LYPCULYCGFOIDA-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E,
F [auth E]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
C [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.82α = 90
b = 105.4β = 90
c = 188.85γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaNSERC-2014-05218

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-04-06
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description