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: 6.00 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.259 

Starting Model: experimental
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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: https://doi.org/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. 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PHOSPHATIDYLINOSITOL 4-KINASE BETA566Homo sapiensMutation(s): 1 
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
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RAS-RELATED PROTEIN RAB-11A219Homo sapiensMutation(s): 1 
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
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RAB11 FAMILY-INTERACTING PROTEIN 348Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75154 (Homo sapiens)
Explore O75154 
Go to UniProtKB:  O75154
PHAROS:  O75154
GTEx:  ENSG00000090565 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75154
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSP
Query on GSP
Download Ideal Coordinates CCD File 
AB [auth P]
DB [auth R]
GB [auth T]
JB [auth X]
LA [auth B]
AB [auth P],
DB [auth R],
GB [auth T],
JB [auth X],
LA [auth B],
MB [auth Z],
OA [auth D],
PB [auth d],
RA [auth H],
SB [auth h],
UA [auth J],
XA [auth N]
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
093
Query on 093
Download Ideal Coordinates CCD File 
CB [auth Q]
FB [auth S]
IB [auth W]
KA [auth A]
LB [auth Y]
CB [auth Q],
FB [auth S],
IB [auth W],
KA [auth A],
LB [auth Y],
NA [auth C],
OB [auth c],
QA [auth G],
RB [auth g],
TA [auth I],
WA [auth M],
ZA [auth O]
N-(5-(4-CHLORO-3-(2-HYDROXY-ETHYLSULFAMOYL)- PHENYLTHIAZOLE-2-YL)-ACETAMIDE
C14 H16 Cl N3 O4 S2
JFVNFXCESCXMBC-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
BB [auth P]
EB [auth R]
HB [auth T]
KB [auth X]
MA [auth B]
BB [auth P],
EB [auth R],
HB [auth T],
KB [auth X],
MA [auth B],
NB [auth Z],
PA [auth D],
QB [auth d],
SA [auth H],
TB [auth h],
VA [auth J],
YA [auth N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
093 BindingDB:  4D0M IC50: min: 19, max: 28 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 6.00 Å
  • R-Value Free: 0.359 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.259 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 199.504α = 90
b = 134.465β = 90.33
c = 294.328γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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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: 2014-06-18
    Changes: Derived calculations
  • Version 1.3: 2018-06-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.4: 2018-11-21
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.5: 2023-12-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description