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PDBsum entry 1d5c

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protein ligands metals links
Endocytosis/exocytosis PDB id
1d5c
Jmol
Contents
Protein chain
162 a.a. *
Ligands
GDP
Metals
_MG
Waters ×63
* Residue conservation analysis
PDB id:
1d5c
Name: Endocytosis/exocytosis
Title: Crystal structure of plasmodium falciparum rab6 complexed with gdp
Structure: Rab6 gtpase. Chain: a. Engineered: yes
Source: Plasmodium falciparum. Malaria parasite p. Falciparum. Organism_taxid: 5833. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.214     R-free:   0.246
Authors: D.Chattopadhyay,G.Langsley,M.Carson,R.Recacha,L.Delucas, C.Smith
Key ref:
D.Chattopadhyay et al. (2000). Structure of the nucleotide-binding domain of Plasmodium falciparum rab6 in the GDP-bound form. Acta Crystallogr D Biol Crystallogr, 56, 937-944. PubMed id: 10944329 DOI: 10.1107/S0907444900007575
Date:
06-Oct-99     Release date:   30-Aug-00    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q26000  (Q26000_PLAFA) -  GTPase (Rab6)
Seq:
Struc:
207 a.a.
162 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: 10.1107/S0907444900007575 Acta Crystallogr D Biol Crystallogr 56:937-944 (2000)
PubMed id: 10944329  
 
 
Structure of the nucleotide-binding domain of Plasmodium falciparum rab6 in the GDP-bound form.
D.Chattopadhyay, G.Langsley, M.Carson, R.Recacha, L.DeLucas, C.Smith.
 
  ABSTRACT  
 
Rab proteins are small Ras-like GTPases which play important roles in regulating intracellular vesicle trafficking. The nucleotide-binding domain of Rab6 from the malaria parasite Plasmodium falciparum was crystallized with GDP bound to the active site. The MAD phasing technique was used to determine the crystal structure to 2.3 A resolution. Comparisons of the structure of GDP-bound PfRab6 with the recently determined structures of Rab3A in complex with either a GTP analog or with GTP and Rabphillin present structural evidence supporting the traditional model for the molecular GTP/GDP switch in Rab proteins. PfRab6 residues homologous to those distinguishing human Rab6 isoforms, which differ in binding to Rabkinesin-6 in human cells, are located next to the recognized complementarity-determining region (CDR) and constitute a conceptual broadening of that domain. Despite significant observable differences in Golgi ultrastructure, the Rab6 core structure and switch mechanism appear highly conserved when compared with murine Rab3a structures. A significant difference between the PfRab6 and higher eukaryotic Rabs may be the lack of CDR features that allow binding interactions with Rabkinesin-type effectors.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 MAD electron-density map. The map computed with experimental MAD phases is shown in stereo contoured at 2.0 . The refined atomic model is shown with the GDP at the left; the silver sphere is Mg2+ and the cyan spheres are coordinated water molecules. All figures were prepared with RIBBONS (Carson, 1997[Carson, M. (1997). Methods Enzymol. 277, 493-505.]), [95]http://www.cmc.uab.edu/ribbons .
Figure 5.
Figure 5 Superposition of Rab6t-GDP and Rab3a-GTP. Ribbon drawings of Rab6t with the Rab3s superposed. The Rab6t ribbon is white, with switch regions pink or orange as in Fig. 3-. The 3rab ribbon is cyan and the 1zbd ribbon is green. The Rab6t-GDP atoms are shown as a ball-and-stick model colored by atom type. The 3rab nucleotide atoms are shown as smaller balls and sticks colored cyan.
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2000, 56, 937-944) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
18243103 A.S.Burguete, T.D.Fenn, A.T.Brunger, and S.R.Pfeffer (2008).
Rab and Arl GTPase family members cooperate in the localization of the golgin GCC185.
  Cell, 132, 286-298.
PDB code: 3bbp
17031879 L.Brunsveld, J.Kuhlmann, K.Alexandrov, A.Wittinghofer, R.S.Goody, and H.Waldmann (2006).
Lipidated ras and rab peptides and proteins--synthesis, structure, and function.
  Angew Chem Int Ed Engl, 45, 6622-6646.  
14978301 C.Blouin, D.Butt, and A.J.Roger (2004).
Rapid evolution in conformational space: a study of loop regions in a ubiquitous GTP binding domain.
  Protein Sci, 13, 608-616.  
15378032 G.Zhu, P.Zhai, J.Liu, S.Terzyan, G.Li, and X.C.Zhang (2004).
Structural basis of Rab5-Rabaptin5 interaction in endocytosis.
  Nat Struct Mol Biol, 11, 975-983.
PDB codes: 1tu3 1tu4
14699104 S.Pasqualato, F.Senic-Matuglia, L.Renault, B.Goud, J.Salamero, and J.Cherfils (2004).
The structural GDP/GTP cycle of Rab11 reveals a novel interface involved in the dynamics of recycling endosomes.
  J Biol Chem, 279, 11480-11488.
PDB codes: 1oiv 1oiw
  11387043 H.Stenmark, and V.M.Olkkonen (2001).
The Rab GTPase family.
  Genome Biol, 2, REVIEWS3007.  
  11071909 A.Echard, F.J.Opdam, H.J.de Leeuw, F.Jollivet, P.Savelkoul, W.Hendriks, J.Voorberg, B.Goud, and J.A.Fransen (2000).
Alternative splicing of the human Rab6A gene generates two close but functionally different isoforms.
  Mol Biol Cell, 11, 3819-3833.  
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 code is shown on the right.