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 
  • R-Value Observed: 0.222 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1038/nsmb832
  • Primary Citation of Related Structures:  
    1TU3, 1TU4

  • 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-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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-5A
A, B, C, D, E
171Homo sapiensMutation(s): 0 
Gene Names: RAB5ARAB5
UniProt & NIH Common Fund Data Resources
Find proteins for P20339 (Homo sapiens)
Explore P20339 
Go to UniProtKB:  P20339
PHAROS:  P20339
GTEx:  ENSG00000144566 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20339
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Rab GTPase binding effector protein 1
F, G, H, I, J
79Homo sapiensMutation(s): 0 
Gene Names: RABEP1RABPT5RABPT5A
UniProt & NIH Common Fund Data Resources
Find proteins for Q15276 (Homo sapiens)
Explore Q15276 
Go to UniProtKB:  Q15276
PHAROS:  Q15276
GTEx:  ENSG00000029725 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15276
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
L [auth A],
N [auth B],
P [auth C],
R [auth D],
T [auth E]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
K [auth A],
M [auth B],
O [auth C],
Q [auth D],
S [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.4α = 90
b = 83.5β = 102.2
c = 144.9γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-10-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description