1TU3

Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural basis of Rab5-Rabaptin5 interaction in endocytosis

Zhu, G., Zhai, P., Liu, J., Terzyan, S., Li, G., Zhang, X.C.

(2004) Nat.Struct.Mol.Biol. 11: 975-983

  • DOI: 10.1038/nsmb832
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Rab5 is a small GTPase that regulates early endosome fusion. We present here the crystal structure of the Rab5 GTPase domain in complex with a GTP analog and the C-terminal domain of effector Rabaptin5. The proteins form a dyad-symmetric Rab5-Rabapti ...

    Rab5 is a small GTPase that regulates early endosome fusion. We present here the crystal structure of the Rab5 GTPase domain in complex with a GTP analog and the C-terminal domain of effector Rabaptin5. The proteins form a dyad-symmetric Rab5-Rabaptin5(2)-Rab5 ternary complex with a parallel coiled-coil Rabaptin5 homodimer in the middle. Two Rab5 molecules bind independently to the Rabaptin5 dimer using their switch and interswitch regions. The binding does not involve the Rab complementarity-determining regions. We also present the crystal structures of two distinct forms of GDP-Rab5 complexes, both of which are incompatible with Rabaptin5 binding. One has a dislocated and disordered switch I but a virtually intact switch II, whereas the other has its beta-sheet and both switch regions reorganized. Biochemical and functional analyses show that the crystallographically observed Rab5-Rabaptin5 complex also exists in solution, and disruption of this complex by mutation abrogates endosome fusion.

    Organizational Affiliation: 

    Crystallography Research Program, Oklahoma Medical Research Foundation, 825 N.E. 13th Street, Oklahoma City, Oklahoma 73104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ras-related protein Rab-5A
A, B, C, D, E
171Homo sapiensMutation(s): 0 
Gene Names: RAB5A (RAB5)
Find proteins for P20339 (Homo sapiens)
Go to Gene View: RAB5A
Go to UniProtKB:  P20339
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Rab GTPase binding effector protein 1
F, G, H, I, J
79Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG
Download SDF File 
Download CCD File 
A, B, C, D, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP
Download SDF File 
Download CCD File 
A, B, C, D, E
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.400α = 90.00
b = 83.500β = 102.20
c = 144.900γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance