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PDBsum entry 1s8f

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protein ligands metals Protein-protein interface(s) links
Protein transport PDB id
1s8f
Jmol
Contents
Protein chains
168 a.a. *
173 a.a. *
Ligands
GDP ×2
BEZ ×4
Metals
_SR ×2
_MG
_CL
Waters ×231
* Residue conservation analysis
PDB id:
1s8f
Name: Protein transport
Title: Crystal structure of rab9 complexed to gdp reveals a dimer with an active conformation of switch ii
Structure: Ras-related protein rab-9a. Chain: a, b. Synonym: rab-9, rab9 gtpase. Engineered: yes. Other_details: c-terminal truncation
Source: Canis lupus familiaris. Dog. Organism_taxid: 9615. Strain: familiaris. Gene: rab9a, rab9. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
1.77Å     R-factor:   0.165     R-free:   0.221
Authors: J.G.Wittmann,M.G.Rudolph
Key ref:
J.G.Wittmann and M.G.Rudolph (2004). Crystal structure of Rab9 complexed to GDP reveals a dimer with an active conformation of switch II. FEBS Lett, 568, 23-29. PubMed id: 15196914 DOI: 10.1016/j.febslet.2004.05.004
Date:
02-Feb-04     Release date:   11-Jun-04    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P24408  (RAB9A_CANFA) -  Ras-related protein Rab-9A
Seq:
Struc:
201 a.a.
168 a.a.
Protein chain
Pfam   ArchSchema ?
P24408  (RAB9A_CANFA) -  Ras-related protein Rab-9A
Seq:
Struc:
201 a.a.
173 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     intracellular   2 terms 
  Biological process     signal transduction   6 terms 
  Biochemical function     GTP binding     2 terms  

 

 
DOI no: 10.1016/j.febslet.2004.05.004 FEBS Lett 568:23-29 (2004)
PubMed id: 15196914  
 
 
Crystal structure of Rab9 complexed to GDP reveals a dimer with an active conformation of switch II.
J.G.Wittmann, M.G.Rudolph.
 
  ABSTRACT  
 
The small GTPase Rab9 is an essential regulator of vesicular transport from the late endosome to the trans-Golgi network, as monitored by the redirection of the mannose-6-phosphate receptors. The crystal structure of Rab9 complexed to GDP, Mg(2+), and Sr(2+) reveals a unique dimer formed by an intermolecular beta-sheet that buries the switch I regions. Surface area and shape complementarity calculations suggest that Rab9 dimers can form an inactive, membrane-bound pool of Rab9 . GDP that is independent of GDI. Mg(2+)-bound Rab9 represents an inactive state, but Sr(2+)-bound Rab9 . GDP displays activated switch region conformations, mimicking those of the GTP state. A hydrophobic tetrad is formed resembling an effector-discriminating epitope found only in GTP-bound Rab proteins.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The Rab9 dimer. The Rab9 asymmetric unit is shown as a ribbon diagram. Molecule A is colored in red (helices) and green (β-strands), molecule B is shown in blue (helices) and pink (β-strands), and coil regions are colored in gray. The nucleotides are drawn as ball-and-stick models and colored according to atom type. Sr^2+, Mg^2+, and Cl^− ions are represented as gray, dark gray, and green spheres, respectively, and the benzoate moieties are drawn as cpk-models. Discontinuities in the structure are marked as dashed lines.
Figure 4.
Fig. 4. Switch regions in Rab structures. (A) Overlay of the switch regions of GDP-bound Rab9 (blue for molecule A and orange for molecule B), Ypt7p (green), Rab11 (yellow), and Ras (gray). Only the ribbon model for Rab9 is shown in light gray for clarity. (B) The effector-binding epitope formed by the switch regions in the GppNHp-bound Rab3A structure is very similar to that present in the GDP-bound Rab9 structure. The Rab3A hydrophobic triad is shown in green, and the residues forming the hydrophobic tetrad in molecule A of Rab9 are drawn in blue. The epitope is not present in molecule B of Rab9 due to the rotation of Phe76 (orange) away from the surface towards the interior of the protein.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2004, 568, 23-29) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22157956 S.Y.Lo, C.L.Brett, R.L.Plemel, M.Vignali, S.Fields, T.Gonen, and A.J.Merz (2012).
Intrinsic tethering activity of endosomal Rab proteins.
  Nat Struct Mol Biol, 19, 40-47.  
19522756 M.T.Lee, A.Mishra, and D.G.Lambright (2009).
Structural mechanisms for regulation of membrane traffic by rab GTPases.
  Traffic, 10, 1377-1389.  
19442299 P.Mackiewicz, and E.Wyroba (2009).
Phylogeny and evolution of Rab7 and Rab9 proteins.
  BMC Evol Biol, 9, 101.  
18458084 F.L.Scott, G.J.Fuchs, S.E.Boyd, J.B.Denault, C.J.Hawkins, F.Dequiedt, and G.S.Salvesen (2008).
Caspase-8 cleaves histone deacetylase 7 and abolishes its transcription repressor function.
  J Biol Chem, 283, 19499-19510.  
17582168 L.M.Chavas, S.Torii, H.Kamikubo, M.Kawasaki, K.Ihara, R.Kato, M.Kataoka, T.Izumi, and S.Wakatsuki (2007).
Structure of the small GTPase Rab27b shows an unexpected swapped dimer.
  Acta Crystallogr D Biol Crystallogr, 63, 769-779.
PDB codes: 2iey 2iez 2if0
15746102 S.R.Pfeffer (2005).
Structural clues to Rab GTPase functional diversity.
  J Biol Chem, 280, 15485-15488.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.