4N3Z

Crystal structure of Rabex-5delta and Rabaptin-5C21 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.264 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular mechanism for Rabex-5 GEF activation by Rabaptin-5

Zhang, Z.Zhang, T.Wang, S.Gong, Z.Tang, C.Chen, J.Ding, J.

(2014) Elife 3: e02687-e02687

  • DOI: 10.7554/eLife.02687
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Rabex-5 and Rabaptin-5 function together to activate Rab5 and further promote early endosomal fusion in endocytosis. The Rabex-5 GEF activity is autoinhibited by the Rabex-5 CC domain (Rabex-5CC) and activated by the Rabaptin-5 C2-1 domain (Rabaptin- ...

    Rabex-5 and Rabaptin-5 function together to activate Rab5 and further promote early endosomal fusion in endocytosis. The Rabex-5 GEF activity is autoinhibited by the Rabex-5 CC domain (Rabex-5CC) and activated by the Rabaptin-5 C2-1 domain (Rabaptin-5C21) with yet unknown mechanism. We report here the crystal structures of Rabex-5 in complex with the dimeric Rabaptin-5C21 (Rabaptin-5C212) and in complex with Rabaptin-5C212 and Rab5, along with biophysical and biochemical analyses. We show that Rabex-5CC assumes an amphipathic α-helix which binds weakly to the substrate-binding site of the GEF domain, leading to weak autoinhibition of the GEF activity. Binding of Rabaptin-5C21 to Rabex-5 displaces Rabex-5CC to yield a largely exposed substrate-binding site, leading to release of the GEF activity. In the ternary complex the substrate-binding site of Rabex-5 is completely exposed to bind and activate Rab5. Our results reveal the molecular mechanism for the regulation of the Rabex-5 GEF activity.


    Organizational Affiliation

    State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rab5 GDP/GTP exchange factor
A
310Homo sapiensMutation(s): 0 
Gene Names: RABGEF1 (RABEX5)
Find proteins for Q9UJ41 (Homo sapiens)
Go to Gene View: RABGEF1
Go to UniProtKB:  Q9UJ41
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Rab GTPase-binding effector protein 1
B, C
92Homo sapiensMutation(s): 0 
Gene Names: RABEP1 (RAB5EP, RABPT5, RABPT5A)
Find proteins for Q15276 (Homo sapiens)
Go to Gene View: RABEP1
Go to UniProtKB:  Q15276
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.264 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 87.140α = 90.00
b = 87.140β = 90.00
c = 168.878γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data collection
PDB_EXTRACTdata extraction
PHASERphasing
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2015-12-09
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description