4D0L

Phosphatidylinositol 4-kinase III beta-PIK93 in a complex with Rab11a- GTP gammaS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structures of Pi4Kiiibeta Complexes Show Simultaneous Recruitment of Rab11 and its Effectors.

Burke, J.E.Inglis, A.J.Perisic, O.Masson, G.R.Mclaughlin, S.H.Rutaganira, F.Shokat, K.M.Williams, R.L.

(2014) Science 344: 1035

  • DOI: 10.1126/science.1253397
  • Primary Citation of Related Structures:  
    4D0L, 4D0M

  • PubMed Abstract: 
  • Phosphatidylinositol 4-kinases (PI4Ks) and small guanosine triphosphatases (GTPases) are essential for processes that require expansion and remodeling of phosphatidylinositol 4-phosphate (PI4P)-containing membranes, including cytokinesis, intracellular development of malarial pathogens, and replication of a wide range of RNA viruses ...

    Phosphatidylinositol 4-kinases (PI4Ks) and small guanosine triphosphatases (GTPases) are essential for processes that require expansion and remodeling of phosphatidylinositol 4-phosphate (PI4P)-containing membranes, including cytokinesis, intracellular development of malarial pathogens, and replication of a wide range of RNA viruses. However, the structural basis for coordination of PI4K, GTPases, and their effectors is unknown. Here, we describe structures of PI4Kβ (PI4KIIIβ) bound to the small GTPase Rab11a without and with the Rab11 effector protein FIP3. The Rab11-PI4KIIIβ interface is distinct compared with known structures of Rab complexes and does not involve switch regions used by GTPase effectors. Our data provide a mechanism for how PI4KIIIβ coordinates Rab11 and its effectors on PI4P-enriched membranes and also provide strategies for the design of specific inhibitors that could potentially target plasmodial PI4KIIIβ to combat malaria.


    Organizational Affiliation

    Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, UK. jeburke@uvic.ca rlw@mrc-lmb.cam.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHATIDYLINOSITOL 4-KINASE BETAA, C, E566Homo sapiensMutation(s): 1 
Gene Names: PI4KBPIK4CB
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
GTEx:  ENSG00000143393 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBF8
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RAS-RELATED PROTEIN RAB-11AB, D, F219Homo sapiensMutation(s): 1 
Gene Names: RAB11ARAB11
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
GTEx:  ENSG00000103769 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62491
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSP
Query on GSP

Download Ideal Coordinates CCD File 
H [auth B],
K [auth D],
N [auth F]
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
 Ligand Interaction
093
Query on 093

Download Ideal Coordinates CCD File 
G [auth A],
J [auth C],
M [auth E]
N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE
C14 H16 Cl N3 O4 S2
JFVNFXCESCXMBC-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth B],
L [auth D],
O [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
093 BindingDB:  4D0L IC50: min: 19, max: 28 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.94 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.795α = 90
b = 146.925β = 90
c = 188.335γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Database references
  • Version 1.2: 2018-06-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations