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 

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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:  
    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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rab-5AA, B, C, D, E171Homo sapiensMutation(s): 0 
Gene Names: RAB5A, RAB5
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P20339 (Homo sapiens)
Explore P20339 
Go to UniProtKB:  P20339
PHAROS:  P20339
GTEx:  ENSG00000144566 
Entity Groups  
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UniProt GroupP20339
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Rab GTPase binding effector protein 1F, G, H, I, J79Homo sapiensMutation(s): 0 
Gene Names: RABEP1, RABPT5, RABPT5A, RAB5EP
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
Protein Feature View
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  • Reference Sequence
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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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