Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 41.19 kDa 
• Atom Count: 3226 
• Modelled Residue Count: 333 
• Deposited Residue Count: 354 
• Unique protein chains: 1

1WMS

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

• PDB DOI: 10.2210/pdb1WMS/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2004-07-16 Released: 2004-09-14 
• Deposition Author(s): Chen, L., DiGiammarino, E., Zhou, X.E., Wang, Y., Toh, D., Hodge, T.W., Meehan, E.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.196 
• R-Value Work: 0.139 
• R-Value Observed: 0.139 

Literature

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

• PubMed: 15263003 
• DOI: 10.1074/jbc.M407114200
• Primary Citation of Related Structures:  
  1WMS


• 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.

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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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-9A	A, B	177	Homo sapiens	Mutation(s): 0  Gene Names: RAB9, RAB9A 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A], D [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 38.4	α = 99.75
b = 45.62	β = 107.17
c = 51.22	γ = 101.84

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
CNS	refinement
SHELXL	refinement
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-16 
• Released Date: 2004-09-14 
Deposition Author(s): Chen, L., DiGiammarino, E., Zhou, X.E., Wang, Y., Toh, D., Hodge, T.W., Meehan, E.J.

Revision History  

• 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