3VVK
An M-like Reaction State of the azide-bound purple form of pharaonis halorhodopsin
Summary for 3VVK
| Entry DOI | 10.2210/pdb3vvk/pdb |
| Related | 3a7k 3abw 3qbi 3qbk 3qbl |
| Descriptor | Halorhodopsin, RETINAL, nonyl beta-D-glucopyranoside, ... (7 entities in total) |
| Functional Keywords | seven-transmembrane-retinylidene protein, chloride-bound purple form, light-driven chloride ion pump, azide-bound purple form, light-driven proton pump, membrane protein |
| Biological source | Natronomonas pharaonis |
| Total number of polymer chains | 6 |
| Total formula weight | 193931.82 |
| Authors | Kouyama, T.,Nakanishi, T. (deposition date: 2012-07-26, release date: 2013-06-19, Last modification date: 2023-11-08) |
| Primary citation | Nakanishi, T.,Kanada, S.,Murakami, M.,Ihara, K.,Kouyama, T. Large deformation of helix F during the photoreaction cycle of Pharaonis halorhodopsin in complex with azide Biophys.J., 104:377-385, 2013 Cited by PubMed Abstract: Halorhodopsin from Natronomonas pharaonis (pHR), a retinylidene protein that functions as a light-driven chloride ion pump, is converted into a proton pump in the presence of azide ion. To clarify this conversion, we investigated light-induced structural changes in pHR using a C2 crystal that was prepared in the presence of Cl(-) and subsequently soaked in a solution containing azide ion. When the pHR-azide complex was illuminated at pH 9, a profound outward movement (∼4 Å) of the cytoplasmic half of helix F was observed in a subunit with the EF loop facing an open space. This movement created a long water channel between the retinal Schiff base and the cytoplasmic surface, along which a proton could be transported. Meanwhile, the middle moiety of helix C moved inward, leading to shrinkage of the primary anion-binding site (site I), and the azide molecule in site I was expelled out to the extracellular medium. The results suggest that the cytoplasmic half of helix F and the middle moiety of helix C act as different types of valves for active proton transport. PubMed: 23442859DOI: 10.1016/j.bpj.2012.12.018 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.3 Å) |
Structure validation
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