PDBsum entry 1d5c

Endocytosis/exocytosis

PDB id: 1d5c

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

Protein chain

Q26000  (Q26000_PLAFA) -  GTPase (Rab6) from Plasmodium falciparum

Seq: 207 a.a.

Struc: 162 a.a.

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.