3CPH
Crystal structure of Sec4 in complex with Rab-GDI
Summary for 3CPH
| Entry DOI | 10.2210/pdb3cph/pdb |
| Related | 3CPI 3CPJ |
| Descriptor | Rab GDP-dissociation inhibitor, Ras-related protein SEC4, MAGNESIUM ION, ... (5 entities in total) |
| Functional Keywords | rab gtpase, prenylation, vesicular transport, cytoplasm, cytoplasmic vesicle, exocytosis, gtp-binding, lipoprotein, membrane, nucleotide-binding, palmitate, phosphoprotein, protein transport, gtpase activation |
| Biological source | Saccharomyces cerevisiae (baker's yeast) More |
| Cellular location | Cytoplasmic vesicle, secretory vesicle membrane; Lipid-anchor; Cytoplasmic side: P39958 Cytoplasm: P07560 |
| Total number of polymer chains | 3 |
| Total formula weight | 126336.36 |
| Authors | Kravchenko, S.,Ignatev, A.,Goody, R.S.,Rak, A.,Pylypenko, O. (deposition date: 2008-03-31, release date: 2008-05-06, Last modification date: 2023-11-01) |
| Primary citation | Ignatev, A.,Kravchenko, S.,Rak, A.,Goody, R.S.,Pylypenko, O. A structural model of the GDP dissociation inhibitor rab membrane extraction mechanism. J.Biol.Chem., 283:18377-18384, 2008 Cited by PubMed Abstract: Rab GDP dissociation inhibitors (GDI)-facilitated extraction of prenylated Rab proteins from membranes plays an important role in vesicular membrane trafficking. The investigated thermodynamic properties of yeast Rab.GDI and Rab.MRS6 complexes demonstrated differences in the Rab binding properties of the closely related Rab GDI and MRS6 proteins, consistent with their functional diversity. The importance of the Rab C terminus and its prenylation for GDI/MRS6 binding was demonstrated using both biochemical and structural data. The presented structures of the apo-form yeast Rab GDI and its two complexes with unprenylated Rab proteins, together with the earlier published structures of the prenylated Ypt1.GDI, provide evidence of allosteric regulation of the GDI lipid binding site opening, which plays a key role in the proposed mechanism of GDI-mediated Rab extraction. We suggest a model for the interaction of GDI with prenylated Rab proteins that incorporates a stepwise increase in affinity as the three different partial interactions are successively formed. PubMed: 18426803DOI: 10.1074/jbc.M709718200 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.9 Å) |
Structure validation
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