3T5G

Structure of fully modified farnesylated Rheb in complex with PDE6D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Arl2-GTP and Arl3-GTP regulate a GDI-like transport system for farnesylated cargo.

Ismail, S.A.Chen, Y.X.Rusinova, A.Chandra, A.Bierbaum, M.Gremer, L.Triola, G.Waldmann, H.Bastiaens, P.I.Wittinghofer, A.

(2011) Nat.Chem.Biol. 7: 942-949

  • DOI: 10.1038/nchembio.686
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lipidated Rho and Rab GTP-binding proteins are transported between membranes in complex with solubilizing factors called 'guanine nucleotide dissociation inhibitors' (GDIs). Unloading from GDIs using GDI displacement factors (GDFs) has been proposed ...

    Lipidated Rho and Rab GTP-binding proteins are transported between membranes in complex with solubilizing factors called 'guanine nucleotide dissociation inhibitors' (GDIs). Unloading from GDIs using GDI displacement factors (GDFs) has been proposed but remains mechanistically elusive. PDEδ is a putative solubilizing factor for several prenylated Ras-subfamily proteins. Here we report the structure of fully modified farnesylated Rheb-GDP in complex with PDEδ. The structure explains the nucleotide-independent binding of Rheb to PDEδ and the relaxed specificity of PDEδ. We demonstrate that the G proteins Arl2 and Arl3 act in a GTP-dependent manner as allosteric release factors for farnesylated cargo. We thus describe a new transport system for farnesylated G proteins involving a GDI-like molecule and an unequivocal GDF. Considering the importance of PDEδ for proper Ras and Rheb signaling, this study is instrumental in developing a new target for anticancer therapy.


    Organizational Affiliation

    Structural Biology Group, Max Planck Institute for Molecular Physiology, Dortmund, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTP-binding protein Rheb
A
181Homo sapiensMutation(s): 1 
Gene Names: RHEB (RHEB2)
Find proteins for Q15382 (Homo sapiens)
Go to Gene View: RHEB
Go to UniProtKB:  Q15382
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
B
152Homo sapiensMutation(s): 0 
Gene Names: PDE6D (PDED)
Find proteins for O43924 (Homo sapiens)
Go to Gene View: PDE6D
Go to UniProtKB:  O43924
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
FAR
Query on FAR

Download SDF File 
Download CCD File 
A
FARNESYL
C15 H26
JXBSHSBNOVLGHF-BUJBXKITSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CMT
Query on CMT
A
L-PEPTIDE LINKINGC4 H9 N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.890α = 90.00
b = 57.380β = 90.00
c = 134.520γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
ProDCdata collection
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-26
    Type: Initial release
  • Version 1.1: 2011-11-30
    Type: Database references
  • Version 1.2: 2013-09-25
    Type: Derived calculations
  • Version 1.3: 2017-11-08
    Type: Refinement description