4D0M

Phosphatidylinositol 4-kinase III beta in a complex with Rab11a-GTP- gamma-S and the Rab-binding domain of FIP3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 6 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


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:  

  • 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, intracellul ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHATIDYLINOSITOL 4-KINASE BETA
A, C, G, I, M, O, Q, S, W, Y, c, g
566Homo sapiensMutation(s): 1 
Gene Names: PI4KB (PIK4CB)
EC: 2.7.1.67
Find proteins for Q9UBF8 (Homo sapiens)
Go to Gene View: PI4KB
Go to UniProtKB:  Q9UBF8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RAS-RELATED PROTEIN RAB-11A
B, D, H, J, N, P, R, T, X, Z, d, h
219Homo sapiensMutation(s): 1 
Gene Names: RAB11A (RAB11)
Find proteins for P62491 (Homo sapiens)
Go to Gene View: RAB11A
Go to UniProtKB:  P62491
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
RAB11 FAMILY-INTERACTING PROTEIN 3
E, F, K, L, U, V, a, b, e, f, i, j
48Homo sapiensMutation(s): 0 
Gene Names: RAB11FIP3 (ARFO1, KIAA0665)
Find proteins for O75154 (Homo sapiens)
Go to Gene View: RAB11FIP3
Go to UniProtKB:  O75154
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
093
Query on 093

Download SDF File 
Download CCD File 
A, c, C, G, g, I, M, O, Q, S, W, Y
N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE
PIK-93; N-[(2Z)-5-(4-CHLORO-3-{[(2-HYDROXYETHYL)AMINO]SULFONYL}PHENYL)-4-METHYL-1,3-THIAZOL-2(3H)-YLIDENE]ACETAMIDE
C14 H16 Cl N3 O4 S2
JFVNFXCESCXMBC-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B, d, D, H, h, J, N, P, R, T, X, Z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GSP
Query on GSP

Download SDF File 
Download CCD File 
B, d, D, h, H, J, N, P, R, T, X, Z
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.253 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 199.504α = 90.00
b = 134.465β = 90.33
c = 294.328γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-28
    Type: Initial release
  • Version 1.1: 2014-06-11
    Type: Database references
  • Version 1.2: 2014-06-18
    Type: Derived calculations
  • Version 1.3: 2018-06-20
    Type: Advisory, Data collection, Derived calculations