crystal structure of human small GTPase Rab7(GTP)

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.249 

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Structural basis for recruitment of RILP by small GTPase Rab7.

Wu, M.Wang, T.Loh, E.Hong, W.Song, H.

(2005) EMBO J 24: 1491-1501

  • DOI: https://doi.org/10.1038/sj.emboj.7600643
  • Primary Citation of Related Structures:  
    1T91, 1YHN

  • PubMed Abstract: 

    Rab7 regulates vesicle traffic from early to late endosomes, and from late endosomes to lysosomes. The crystal structure of Rab7-GTP in complex with the Rab7 binding domain of RILP reveals that Rab7 interacts with RILP specifically via two distinct areas, with the first one involving the switch and interswitch regions and the second one consisting of RabSF1 and RabSF4. Disruption of these interactions by mutations abrogates late endosomal/lysosomal targeting of Rab7 and RILP. The Rab7 binding domain of RILP forms a coiled-coil homodimer with two symmetric surfaces to interact with two separate Rab7-GTP molecules, forming a dyad configuration of Rab7-RILP(2)-Rab7. Mutations that disrupt RILP dimerization also abolish its interactions with Rab7-GTP and late endosomal/lysosomal targeting, suggesting that the dimeric form of RILP is a functional unit. Structural comparison suggests that the combined use of RabSF1 and RabSF4 with the switch regions may be a general mode of action for most Rab proteins in regulating membrane trafficking.

  • Organizational Affiliation

    Laboratory of Macromolecular Structure, Institute of Molecular and Cell Biology, Proteos, Singapore.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-7
A, B, C, D
207Homo sapiensMutation(s): 1 
Gene Names: Rab7
UniProt & NIH Common Fund Data Resources
Find proteins for P51149 (Homo sapiens)
Explore P51149 
Go to UniProtKB:  P51149
PHAROS:  P51149
GTEx:  ENSG00000075785 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51149
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.249 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.695α = 71.51
b = 56.777β = 71.72
c = 74.51γ = 77.75
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CCP4data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-05-17
    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: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description