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Crystal structure of the ligand-free G-protein-coupled receptor opsin

Abstract

In the G-protein-coupled receptor (GPCR) rhodopsin, the inactivating ligand 11-cis-retinal is bound in the seven-transmembrane helix (TM) bundle and is cis/trans isomerized by light to form active metarhodopsin II. With metarhodopsin II decay, all-trans-retinal is released, and opsin is reloaded with new 11-cis-retinal. Here we present the crystal structure of ligand-free native opsin from bovine retinal rod cells at 2.9 ångström (Å) resolution. Compared to rhodopsin, opsin shows prominent structural changes in the conserved E(D)RY and NPxxY(x)5,6F regions and in TM5–TM7. At the cytoplasmic side, TM6 is tilted outwards by 6–7 Å, whereas the helix structure of TM5 is more elongated and close to TM6. These structural changes, some of which were attributed to an active GPCR state, reorganize the empty retinal-binding pocket to disclose two openings that may serve the entry and exit of retinal. The opsin structure sheds new light on ligand binding to GPCRs and on GPCR activation.

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Figure 1: Overall fold of opsin.
Figure 2: Structure of opsin and comparison with rhodopsin.
Figure 3: Superposition of conserved E(D)RY regions of rhodopsin and opsin.
Figure 4: Superposition of conserved NPxxY(x) 5,6 F regions of rhodopsin and opsin.
Figure 5: Retinal-binding pocket.
Figure 6: Openings of the retinal-binding pocket in opsin.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The coordinates and structure factors have been deposited in the Protein Data Bank under accession number 3CAP.

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Acknowledgements

We thank J. Engelmann and C. Koch for technical assistance; Y. Li for help in the early stage of the project; Y. J. Kim for help with data collection; M. Sommer, C. Enenkel and M. Heck for critically reading the manuscript; and N. Krauss for support and sharing his expertise in crystallography. We thank U. Müller and the scientific staff of the Protein Structure Factory and the Freie Universität Berlin at beamlines BL 14.1 and BL 14.2 at BESSY for continuous support of the project. This work was supported by the Deutsche Forschungsgemeinschaft Sfb449 (to O.P.E.), Sfb740 (to O.P.E. and K.P.H.), DFG-KOSEF international cooperation ER 294/1-1 (to O.P.E.) and F01-2004-000-10054-0 (to H.-W.C.). H-.W.C. was supported by CBNU funds for overseas research 2006–2007.

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Correspondence to Klaus Peter Hofmann, Hui-Woog Choe or Oliver Peter Ernst.

Supplementary information

Supplementary Information

This file contains Supplementary Table 1, Supplementary Discussion and Supplementary Figure 1. Supplementary Table 1 includes X-ray data collection and refinement statistics. A model of rhodopsin regeneration shown in Supplementary Figure 1 is discussed. (PDF 468 kb)

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Park, J., Scheerer, P., Hofmann, K. et al. Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature 454, 183–187 (2008). https://doi.org/10.1038/nature07063

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