High resolution crystal structure of human Rab9 GTPase: a novel antiviral drug target

Experimental Data Snapshot

  • Resolution: 1.25 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.139 

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High resolution crystal structure of human Rab9 GTPase: A novel antiviral drug target

Chen, L.DiGiammarino, E.Zhou, X.E.Wang, Y.Toh, D.Hodge, T.W.Meehan, E.J.

(2004) J Biol Chem 279: 40204-40208

  • DOI: https://doi.org/10.1074/jbc.M407114200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Rab GTPases and their effectors facilitate vesicular transport by tethering donor vesicles to their respective target membranes. Rab9 mediates late endosome to trans-Golgi transport and has recently been found to be a key cellular component for human immunodeficiency virus-1, Ebola, Marburg, and measles virus replication, suggesting that it may be a novel target in the development of broad spectrum antiviral drugs. As part of our structure-based drug design program, we have determined the crystal structure of a C-terminally truncated human Rab9 (residues 1-177) to 1.25-A resolution. The overall structure shows a characteristic nucleotide binding fold consisting of a six-stranded beta-sheet surrounded by five alpha-helices with a tightly bound GDP molecule in the active site. Structure-based sequence alignment of Rab9 with other Rab proteins reveals that its active site consists of residues highly conserved in the Rab GTPase family, implying a common catalytic mechanism. However, Rab9 contains seven regions that are significantly different in conformation from other Rab proteins. Some of those regions coincide with putative effector-binding sites and switch I and switch II regions identified by structure/sequence alignments. The Rab9 structure at near atomic resolution provides an excellent model for structure-based antiviral drug design.

  • Organizational Affiliation

    Laboratory for Structural Biology, Department of Chemistry, Graduate Programs of Biotechnology, Chemistry and Materials Science, University of Alabama in Huntsville, Huntsville, Alabama 35899, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein Rab-9A
A, B
177Homo sapiensMutation(s): 0 
Gene Names: Rab9
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P51151 (Homo sapiens)
Explore P51151 
Go to UniProtKB:  P51151
PHAROS:  P51151
GTEx:  ENSG00000123595 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51151
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 1.25 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.139 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.4α = 99.75
b = 45.62β = 107.17
c = 51.22γ = 101.84
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-14
    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: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description