5MY3

Crystal structure of the RhoGAP domain of Rgd1p at 2.19 Angstroms resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 

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This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:4U3K


Literature

Structural evidence of a phosphoinositide-binding site in the Rgd1-RhoGAP domain.

Martinez, D.Langlois d'Estaintot, B.Granier, T.Tolchard, J.Courreges, C.Prouzet-Mauleon, V.Hugues, M.Gallois, B.Doignon, F.Odaert, B.

(2017) Biochem J 474: 3307-3319

  • DOI: 10.1042/BCJ20170331
  • Primary Citation of Related Structures:  
    5MY3

  • PubMed Abstract: 
  • Phosphoinositide lipids recruit proteins to the plasma membrane involved in the regulation of cytoskeleton organization and in signalling pathways that control cell polarity and growth. Among those, Rgd1p is a yeast GTPase-activating protein (GAP) specific for Rho3p and Rho4p GTPases, which control actin polymerization and stress signalling pathways ...

    Phosphoinositide lipids recruit proteins to the plasma membrane involved in the regulation of cytoskeleton organization and in signalling pathways that control cell polarity and growth. Among those, Rgd1p is a yeast GTPase-activating protein (GAP) specific for Rho3p and Rho4p GTPases, which control actin polymerization and stress signalling pathways. Phosphoinositides not only bind Rgd1p, but also stimulate its GAP activity on the membrane-anchored form of Rho4p. Both F-BAR (F-BAR FCH, and BAR) and RhoGAP domains of Rgd1p are involved in lipid interactions. In the Rgd1p-F-BAR domain, a phosphoinositide-binding site has been recently characterized. We report here the X-ray structure of the Rgd1p-RhoGAP domain, identify by NMR spectroscopy and confirm by docking simulations, a new but cryptic phosphoinositide-binding site, comprising contiguous A1, A1' and B helices. The addition of helix A1', unusual among RhoGAP domains, seems to be crucial for lipid interactions. Such a site was totally unexpected inside a RhoGAP domain, as it was not predicted from either the protein sequence or its three-dimensional structure. Phosphoinositide-binding sites in RhoGAP domains have been reported to correspond to polybasic regions, which are located at the unstructured flexible termini of proteins. Solid-state NMR spectroscopy experiments confirm the membrane interaction of the Rgd1p-RhoGAP domain upon the addition of PtdIns(4,5)P 2 and indicate a slight membrane destabilization in the presence of the two partners.


    Organizational Affiliation

    Université de Bordeaux, Chimie et Biologie des Membranes et des Nano-objets, CNRS UMR 5248, Allée Geoffroy Saint Hilaire, 33600 Pessac Cedex, France b.odaert@cbmn.u-bordeaux.fr francois.doignon@u-bordeaux.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RHO GTPase-activating protein RGD1A226Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RGD1YBR260CYBR1728
UniProt
Find proteins for P38339 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38339 
Go to UniProtKB:  P38339
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.23α = 90
b = 63.23β = 90
c = 99.73γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-24
    Type: Initial release