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      Crystal structure of rhodopsin in complex with a mini-G o sheds light on the principles of G protein selectivity

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          Abstract

          The structure of the rhodopsin/mini-G o complex reveals new insights on G protein selectivity.

          Abstract

          Selective coupling of G protein (heterotrimeric guanine nucleotide–binding protein)–coupled receptors (GPCRs) to specific Gα-protein subtypes is critical to transform extracellular signals, carried by natural ligands and clinical drugs, into cellular responses. At the center of this transduction event lies the formation of a signaling complex between the receptor and G protein. We report the crystal structure of light-sensitive GPCR rhodopsin bound to an engineered mini-G o protein. The conformation of the receptor is identical to all previous structures of active rhodopsin, including the complex with arrestin. Thus, rhodopsin seems to adopt predominantly one thermodynamically stable active conformation, effectively acting like a “structural switch,” allowing for maximum efficiency in the visual system. Furthermore, our analysis of the well-defined GPCR–G protein interface suggests that the precise position of the carboxyl-terminal “hook-like” element of the G protein (its four last residues) relative to the TM7/helix 8 (H8) joint of the receptor is a significant determinant in selective G protein activation.

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          Most cited references40

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          Crystal structure of opsin in its G-protein-interacting conformation.

          Opsin, the ligand-free form of the G-protein-coupled receptor rhodopsin, at low pH adopts a conformationally distinct, active G-protein-binding state known as Ops*. A synthetic peptide derived from the main binding site of the heterotrimeric G protein-the carboxy terminus of the alpha-subunit (GalphaCT)-stabilizes Ops*. Here we present the 3.2 A crystal structure of the bovine Ops*-GalphaCT peptide complex. GalphaCT binds to a site in opsin that is opened by an outward tilt of transmembrane helix (TM) 6, a pairing of TM5 and TM6, and a restructured TM7-helix 8 kink. Contacts along the inner surface of TM5 and TM6 induce an alpha-helical conformation in GalphaCT with a C-terminal reverse turn. Main-chain carbonyl groups in the reverse turn constitute the centre of a hydrogen-bonded network, which links the two receptor regions containing the conserved E(D)RY and NPxxY(x)(5,6)F motifs. On the basis of the Ops*-GalphaCT structure and known conformational changes in Galpha, we discuss signal transfer from the receptor to the G protein nucleotide-binding site.
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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). The photoreceptor rhodopsin couples to transducin and bears its ligand 11-cis-retinal covalently bound via a protonated Schiff base to the opsin apoprotein. 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 subunit. 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*) 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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              Crystal structure of the ligand-free G-protein-coupled receptor opsin.

              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 (A) resolution. Compared to rhodopsin, opsin shows prominent structural changes in the conserved E(D)RY and NPxxY(x)(5,6)F regions and in TM5-TM7. At the cytoplasmic side, TM6 is tilted outwards by 6-7 A, 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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                Author and article information

                Journal
                Sci Adv
                Sci Adv
                SciAdv
                advances
                Science Advances
                American Association for the Advancement of Science
                2375-2548
                September 2018
                19 September 2018
                : 4
                : 9
                : eaat7052
                Affiliations
                [1 ]Laboratory of Biomolecular Research, Paul Scherrer Institute (PSI), 5232 Villigen PSI, Switzerland.
                [2 ]Department of Biology, ETH Zürich, Wolfgang-Pauli-Strasse 27, 8093 Zürich, Switzerland.
                [3 ]Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
                [4 ]Fitzwilliam College, University of Cambridge, Cambridge, UK.
                [5 ]Condensed Matter Theory Group, PSI, 5232 Villigen PSI, Switzerland.
                Author notes
                [* ]Corresponding author. Email: ching-ju.tsai@ 123456psi.ch (C.-J.T.); gebhard.schertler@ 123456psi.ch (G.F.X.S.)
                [†]

                Present address: Creoptix AG, Einsiedlerstrasse 34, 8820 Wädenswil, Switzerland.

                [‡]

                Present address: Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK.

                Author information
                http://orcid.org/0000-0001-8320-5009
                http://orcid.org/0000-0002-0339-3722
                http://orcid.org/0000-0003-3398-0968
                http://orcid.org/0000-0002-8040-7753
                http://orcid.org/0000-0003-1712-3528
                http://orcid.org/0000-0003-4080-2908
                http://orcid.org/0000-0003-4572-9316
                http://orcid.org/0000-0001-8825-386X
                http://orcid.org/0000-0002-2008-9183
                http://orcid.org/0000-0002-5846-6810
                Article
                aat7052
                10.1126/sciadv.aat7052
                6154990
                30255144
                8a717ac9-cc72-41fa-8970-71988692d899
                Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).

                This is an open-access article distributed under the terms of the Creative Commons Attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 26 March 2018
                : 10 August 2018
                Funding
                Funded by: doi http://dx.doi.org/10.13039/501100000265, Medical Research Council;
                Award ID: MRC U105197215
                Funded by: doi http://dx.doi.org/10.13039/501100000781, European Research Council;
                Award ID: EMPSI 339995
                Funded by: doi http://dx.doi.org/10.13039/501100001711, Swiss National Science Foundation;
                Award ID: 310030_153145
                Funded by: doi http://dx.doi.org/10.13039/501100001711, Swiss National Science Foundation;
                Award ID: 310030B_173335
                Funded by: doi http://dx.doi.org/10.13039/501100001711, Swiss National Science Foundation;
                Award ID: PZ00P3_174169
                Funded by: doi http://dx.doi.org/10.13039/501100001711, Swiss National Science Foundation;
                Award ID: 31003A_159558
                Funded by: Heptares Therapeutics;
                Funded by: doi http://dx.doi.org/10.13039/501100001711, Swiss National Science Foundation;
                Award ID: 160805
                Funded by: ETH Zürich Fellowship;
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