6DJL

Crystal structure of the Rab11 GEF SH3BP5 bound to nucleotide free Rab11A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10001 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural determinants of Rab11 activation by the guanine nucleotide exchange factor SH3BP5.

Jenkins, M.L.Margaria, J.P.Stariha, J.T.B.Hoffmann, R.M.McPhail, J.A.Hamelin, D.J.Boulanger, M.J.Hirsch, E.Burke, J.E.

(2018) Nat Commun 9: 3772-3772

  • DOI: 10.1038/s41467-018-06196-z

  • PubMed Abstract: 
  • The GTPase Rab11 plays key roles in receptor recycling, oogenesis, autophagosome formation, and ciliogenesis. However, investigating Rab11 regulation has been hindered by limited molecular detail describing activation by cognate guanine nucleotide ex ...

    The GTPase Rab11 plays key roles in receptor recycling, oogenesis, autophagosome formation, and ciliogenesis. However, investigating Rab11 regulation has been hindered by limited molecular detail describing activation by cognate guanine nucleotide exchange factors (GEFs). Here, we present the structure of Rab11 bound to the GEF SH3BP5, along with detailed characterization of Rab-GEF specificity. The structure of SH3BP5 shows a coiled-coil architecture that mediates exchange through a unique Rab-GEF interaction. Furthermore, it reveals a rearrangement of the switch I region of Rab11 compared with solved Rab-GEF structures, with a constrained conformation when bound to SH3BP5. Mutation of switch I provides insights into the molecular determinants that allow for Rab11 selectivity over evolutionarily similar Rab GTPases present on Rab11-positive organelles. Moreover, we show that GEF-deficient mutants of SH3BP5 show greatly decreased Rab11 activation in cellular assays of active Rab11. Overall, our results give molecular insight into Rab11 regulation, and how Rab-GEF specificity is achieved.


    Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 2Y2, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rab-11A
A, F, G, 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: 2
MoleculeChainsSequence LengthOrganismDetails
SH3 domain-binding protein 5
B, C, D, E
266Homo sapiensMutation(s): 0 
Gene Names: SH3BP5 (SAB)
Find proteins for O60239 (Homo sapiens)
Go to Gene View: SH3BP5
Go to UniProtKB:  O60239
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10001 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.235 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 114.850α = 90.00
b = 197.040β = 90.00
c = 304.710γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CRANK2phasing
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (Canada)Canada05214

Revision History 

  • Version 1.0: 2018-09-26
    Type: Initial release