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Crystal structure of metarhodopsin II


G-protein-coupled receptors (GPCRs) are seven transmembrane helix (TM) proteins that transduce signals into living cells by binding extracellular ligands and coupling to intracellular heterotrimeric G proteins (Gαβγ)1. The photoreceptor rhodopsin couples to transducin and bears its ligand 11-cis-retinal covalently bound via a protonated Schiff base to the opsin apoprotein2. Absorption of a photon causes retinal cis/trans isomerization and generates the agonist all-trans-retinal in situ. After early photoproducts, the active G-protein-binding intermediate metarhodopsin II (Meta II) is formed, in which the retinal Schiff base is still intact but deprotonated. Dissociation of the proton from the Schiff base breaks a major constraint in the protein and enables further activating steps, including an outward tilt of TM6 and formation of a large cytoplasmic crevice for uptake of the interacting C terminus of the Gα subunit3,4,5. Owing to Schiff base hydrolysis, Meta II is short-lived and notoriously difficult to crystallize. We therefore soaked opsin crystals with all-trans-retinal to form Meta II, presuming that the crystal’s high concentration of opsin in an active conformation (Ops*)6,7 may facilitate all-trans-retinal uptake and Schiff base formation. Here we present the 3.0 Å and 2.85 Å crystal structures, respectively, of Meta II alone or in complex with an 11-amino-acid C-terminal fragment derived from Gα (GαCT2). GαCT2 binds in a large crevice at the cytoplasmic side, akin to the binding of a similar Gα-derived peptide to Ops* (ref. 7). In the Meta II structures, the electron density from the retinal ligand seamlessly continues into the Lys 296 side chain, reflecting proper formation of the Schiff base linkage. The retinal is in a relaxed conformation and almost undistorted compared with pure crystalline all-trans-retinal. By comparison with early photoproducts we propose how retinal translocation and rotation induce the gross conformational changes characteristic for Meta II. The structures can now serve as models for the large GPCR family.

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Figure 1: Structures of inactive rhodopsin, active Meta II and Meta II in complex with a Gα fragment.
Figure 2: Retinal binding pocket of Meta II.
Figure 3: Superposition of rhodopsin, Batho, Lumi and Meta II.
Figure 4: Conserved E(D)RY and NPxxY(x) 5,6 F regions.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported structure have been deposited in the Protein Data Bank with the accession codes 3PQR and 3PXO.


  1. Rosenbaum, D. M., Rasmussen, S. G. & Kobilka, B. K. The structure and function of G-protein-coupled receptors. Nature 459, 356–363 (2009)

    Article  CAS  ADS  Google Scholar 

  2. Palczewski, K. G protein-coupled receptor rhodopsin. Annu. Rev. Biochem. 75, 743–767 (2006)

    Article  CAS  Google Scholar 

  3. Altenbach, C., Kusnetzow, A. K., Ernst, O. P., Hofmann, K. P. & Hubbell, W. L. High-resolution distance mapping in rhodopsin reveals the pattern of helix movement due to activation. Proc. Natl Acad. Sci. USA 105, 7439–7444 (2008)

    Article  CAS  ADS  Google Scholar 

  4. Hofmann, K. P. et al. A G protein-coupled receptor at work: the rhodopsin model. Trends Biochem. Sci. 34, 540–552 (2009)

    Article  CAS  Google Scholar 

  5. Choe, H.-W., Park, J. H., Kim, Y. J. & Ernst, O. P. Transmembrane signaling by GPCRs: insight from rhodopsin and opsin structures. Neuropharmacology 60, 52–57 (2011)

    Article  CAS  Google Scholar 

  6. Park, J. H., Scheerer, P., Hofmann, K. P., Choe, H.-W. & Ernst, O. P. Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature 454, 183–187 (2008)

    Article  CAS  ADS  Google Scholar 

  7. Scheerer, P. et al. Crystal structure of opsin in its G-protein-interacting conformation. Nature 455, 497–502 (2008)

    Article  CAS  ADS  Google Scholar 

  8. Palczewski, K. et al. Crystal structure of rhodopsin: a G protein-coupled receptor. Science 289, 739–745 (2000)

    Article  CAS  ADS  Google Scholar 

  9. Okada, T. et al. The retinal conformation and its environment in rhodopsin in light of a new 2.2 Å crystal structure. J. Mol. Biol. 342, 571–583 (2004)

    Article  CAS  Google Scholar 

  10. Li, J., Edwards, P. C., Burghammer, M., Villa, C. & Schertler, G. F. Structure of bovine rhodopsin in a trigonal crystal form. J. Mol. Biol. 343, 1409–1438 (2004)

    Article  CAS  Google Scholar 

  11. Siebert, F. Application of FTIR spectroscopy to the investigation of dark structures and photoreactions of visual pigments. Isr. J. Chem. 35, 309–323 (1995)

    Article  CAS  Google Scholar 

  12. Lüdeke, S. et al. The role of Glu181 in the photoactivation of rhodopsin. J. Mol. Biol. 353, 345–356 (2005)

    Article  Google Scholar 

  13. Angel, T. E., Chance, M. R. & Palczewski, K. Conserved waters mediate structural and functional activation of family A (rhodopsin-like) G protein-coupled receptors. Proc. Natl Acad. Sci. USA 106, 8555–8560 (2009)

    Article  CAS  ADS  Google Scholar 

  14. Angel, T. E., Gupta, S., Jastrzebska, B., Palczewski, K. & Chance, M. R. Structural waters define a functional channel mediating activation of the GPCR, rhodopsin. Proc. Natl Acad. Sci. USA 106, 14367–14372 (2009)

    Article  CAS  ADS  Google Scholar 

  15. Hildebrand, P. W. et al. A ligand channel through the G protein coupled receptor opsin. PLoS ONE 4, e4382 (2009)

    Article  ADS  Google Scholar 

  16. Ahuja, S. et al. Helix movement is coupled to displacement of the second extracellular loop in rhodopsin activation. Nature Struct. Mol. Biol. 16, 168–175 (2009)

    Article  CAS  Google Scholar 

  17. Smith, S. O. Structure and activation of the visual pigment rhodopsin. Annu. Rev. Biophys. 39, 309–328 (2010)

    Article  CAS  Google Scholar 

  18. Nakamichi, H. & Okada, T. Crystallographic analysis of primary visual photochemistry. Angew. Chem. Int. Edn Engl. 45, 4270–4273 (2006)

    Article  CAS  Google Scholar 

  19. Nakamichi, H. & Okada, T. Local peptide movement in the photoreaction intermediate of rhodopsin. Proc. Natl Acad. Sci. USA 103, 12729–12734 (2006)

    Article  CAS  ADS  Google Scholar 

  20. Ye, S. et al. Tracking G-protein-coupled receptor activation using genetically encoded infrared probes. Nature 464, 1386–1389 (2010)

    Article  CAS  ADS  Google Scholar 

  21. Shi, L. et al. β2 adrenergic receptor activation. Modulation of the proline kink in transmembrane 6 by a rotamer toggle switch. J. Biol. Chem. 277, 40989–40996 (2002)

    Article  CAS  Google Scholar 

  22. Crocker, E. et al. Location of Trp265 in metarhodopsin II: implications for the activation mechanism of the visual receptor rhodopsin. J. Mol. Biol. 357, 163–172 (2006)

    Article  CAS  Google Scholar 

  23. Nygaard, R., Frimurer, T. M., Holst, B., Rosenkilde, M. M. & Schwartz, T. W. Ligand binding and micro-switches in 7TM receptor structures. Trends Pharmacol. Sci. 30, 249–259 (2009)

    Article  CAS  Google Scholar 

  24. Salgado, G. F. et al. Solid-state 2H NMR structure of retinal in metarhodopsin I. J. Am. Chem. Soc. 128, 11067–11071 (2006)

    Article  CAS  Google Scholar 

  25. Ahuja, S. et al. 6-s-cis conformation and polar binding pocket of the retinal chromophore in the photoactivated state of rhodopsin. J. Am. Chem. Soc. 131, 15160–15169 (2009)

    Article  CAS  Google Scholar 

  26. Brown, M. F., Salgado, G. F. & Struts, A. V. Retinal dynamics during light activation of rhodopsin revealed by solid-state NMR spectroscopy. Biochim. Biophys. Acta 1798, 177–193 (2010)

    Article  CAS  Google Scholar 

  27. Lau, P. W., Grossfield, A., Feller, S. E., Pitman, M. C. & Brown, M. F. Dynamic structure of retinylidene ligand of rhodopsin probed by molecular simulations. J. Mol. Biol. 372, 906–917 (2007)

    Article  CAS  Google Scholar 

  28. Fujimoto, Y. et al. On the bioactive conformation of the rhodopsin chromophore: absolute sense of twist around the 6-s-cis bond. Chem. Eur. J. 7, 4198–4204 (2001)

    Article  CAS  Google Scholar 

  29. Knierim, B., Hofmann, K. P., Gartner, W., Hubbell, W. L. & Ernst, O. P. Rhodopsin and 9-demethyl-retinal analog: effect of a partial agonist on displacement of transmembrane helix 6 in class A G protein-coupled receptors. J. Biol. Chem. 283, 4967–4974 (2008)

    Article  CAS  Google Scholar 

  30. Ballesteros, J. A. & Weinstein, H. Integrated methods for the construction of three-dimensional models and computational probing of structure-function relations in G-protein coupled receptors. Methods Neurosci. 25, 366–428 (1995)

    Article  CAS  Google Scholar 

  31. Herrmann, R. et al. Sequence of interactions in receptor-G protein coupling. J. Biol. Chem. 279, 24283–24290 (2004)

    Article  CAS  Google Scholar 

  32. Kabsch, W. XDS. Acta Crystallogr. D 66, 125–132 (2010)

    Article  CAS  Google Scholar 

  33. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994)

  34. Brünger, A. T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

    Article  Google Scholar 

  35. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004)

    Article  Google Scholar 

  36. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283–291 (1993)

    Article  CAS  Google Scholar 

  37. Hooft, R. W., Vriend, G., Sander, C. & Abola, E. E. Errors in protein structures. Nature 381, 272 (1996)

    Article  CAS  ADS  Google Scholar 

  38. McDonald, I. K. & Thornton, J. M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 238, 777–793 (1994)

    Article  CAS  Google Scholar 

  39. Wallace, A. C., Laskowski, R. A. & Thornton, J. M. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 8, 127–134 (1995)

    Article  CAS  Google Scholar 

  40. DeLano, W. L. The PyMOL Molecular Graphics System. (DeLano Scientific, San Carlos, California, USA, 2002)

  41. Fahmy, K. & Sakmar, T. P. Regulation of the rhodopsin-transducin interaction by a highly conserved carboxylic acid group. Biochemistry 32, 7229–7236 (1993)

    Article  CAS  Google Scholar 

  42. Ernst, O. P., Bieri, C., Vogel, H. & Hofmann, K. P. Intrinsic biophysical monitors of transducin activation: fluorescence, UV-visible spectroscopy, light scattering, and evanescent field techniques. Methods Enzymol. 315, 471–489 (2000)

    Article  CAS  Google Scholar 

  43. Ernst, O. P., Gramse, V., Kolbe, M., Hofmann, K. P. & Heck, M. Monomeric G protein-coupled receptor rhodopsin in solution activates its G protein transducin at the diffusion limit. Proc. Natl Acad. Sci. USA 104, 10859–10864 (2007)

    Article  CAS  ADS  Google Scholar 

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We thank J. Engelmann, C. Koch and B. Bauer for technical assistance, and F. Siebert and W. Hubbell for critically reading the manuscript. We are grateful to the European Synchrotron Radiation Facility (ESRF, Grenoble), D. von Stetten and A. Royant of the ID29S-Cryobench (ESRF, Grenoble) and U. Müller and the scientific staff of the BESSY-MX/Helmholtz Zentrum Berlin für Materialien und Energie at beamlines BL 14.1 and BL 14.2, where the data were collected, for continuous support. This work was supported by the DFG Sfb449 (to O.P.E.), Sfb740 (to O.P.E. and K.P.H.) and an Advanced Investigator ERC grant (to K.P.H.) and by the Canada Research Chairs Program (to E.F.P.). H.-W.C. gratefully acknowledges the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (2010-0002738) and CBNU funds for overseas research 2009. Y.J.K. thanks the Leibniz Graduate School of Molecular Biophysics, Berlin, for a scholarship.

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Authors and Affiliations



H.-W.C., Y.J.K. and J.H.P. are joint first authors. H.-W.C., Y.J.K., J.H.P. performed preparation and crystallization of opsin/opsin−GαCT2. H.-W.C. performed the soaking experiment of both crystals. O.P.E. designed GαCT2. H.-W.C., Y.J.K., J.H.P., P.S., O.P.E. performed the data collection. Y.J.K., P.S., N.K. performed the structural analysis of Meta II, and J.H.P., P.S., E.F.P. performed the structural analysis of Meta II·GαCT2. T.M. performed the spectroscopic and biochemical analysis. H.-W.C., N.K., K.P.H., P.S., O.P.E. analysed data and H.-W.C., K.P.H., O.P.E. wrote the paper with contributions from all authors.

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

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The authors declare no competing financial interests.

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This file contains Supplementary Figures 1-10 with legends, Supplementary Tables 1-2, a Supplementary Discussion and additional references. (PDF 8968 kb)

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Choe, HW., Kim, Y., Park, J. et al. Crystal structure of metarhodopsin II. Nature 471, 651–655 (2011).

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