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Structure of class C GPCR metabotropic glutamate receptor 5 transmembrane domain

Abstract

Metabotropic glutamate receptors are class C G-protein-coupled receptors which respond to the neurotransmitter glutamate. Structural studies have been restricted to the amino-terminal extracellular domain, providing little understanding of the membrane-spanning signal transduction domain. Metabotropic glutamate receptor 5 is of considerable interest as a drug target in the treatment of fragile X syndrome, autism, depression, anxiety, addiction and movement disorders. Here we report the crystal structure of the transmembrane domain of the human receptor in complex with the negative allosteric modulator, mavoglurant. The structure provides detailed insight into the architecture of the transmembrane domain of class C receptors including the precise location of the allosteric binding site within the transmembrane domain and key micro-switches which regulate receptor signalling. This structure also provides a model for all class C G-protein-coupled receptors and may aid in the design of new small-molecule drugs for the treatment of brain disorders.

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Figure 1: Schematic and ribbon representation of the mGlu5 structure.
Figure 2: The narrow entrance to the allosteric pocket in mGlu5.
Figure 3: Superposition and comparison of mGlu5 with rhodopsin and CRF1R.
Figure 4: The ‘ionic-lock’ motifs in mGlu5 and rhodopsin.
Figure 5: Molecular details of further conserved sequence motifs in mGlu5 and comparison to rhodopsin.
Figure 6: The mGlu5 allosteric modulator binding site.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Co-ordinates and structure factors have been deposited in the Protein Data Bank under the accession code 4OO9.

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Acknowledgements

We thank R. Owen, J. Waterman and D. Axford at I24, Diamond Light Source, Oxford, UK for technical support. We thank C. G. Tate and other colleagues at Heptares Therapeutics Ltd for suggestions and comments, specifically K. Hollenstein and R. Cheng for contributions to the crystallography, and J. Christopher and G. Brown for sourcing allosteric ligands.

Author information

Authors and Affiliations

Authors

Contributions

J.C.P., G.R.W. and S.K. carried out the conformational thermostabilization of the constructs and determined the stability of the StaR in a panel of reagents/additives to aid purification and crystallization. K.B. carried out the pharmacology. A.J. devised the stabilization strategy and designed the T4L fusion matrix. A.J. and J.C.P. carried out functional analyses the mutants. J.C.E. contributed to construct design and purification strategy. M.S.-V. characterized truncation constructs and established procedures for, and carried out expression and purification. K.O. performed expression, purification, LCP crystallization, optimized purification and performed crystallization in LCP for data collection of the final construct. A.S.D. designed crystallization constructs, established the platform/protocols for, and carried out LCP crystallization and designed crystal optimization, harvested crystals, collected and processed X-ray diffraction data, solved and refined the structure, and devised functional mutations. Computational analysis of the structure and modelling was carried out by B.T. and A.S.D. Project management was carried out by A.J., R.M.C., M.W. and F.H.M. The manuscript was prepared by A.S.D., B.T., A.J., R.M.C., K.B. and F.H.M.

Corresponding author

Correspondence to Fiona H. Marshall.

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The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Comparison of wild-type and thermostabilized mGlu5.

a, The thermal stability of mGlu5 constructs measured using [3H] M-MPEP binding following DDM solubilization. Wild-type full-length mGlu5 (closed circles) has a Tm of 20.6 ± 1.6 °C and mGlu5StaR 569–836-T4L (open circles) has a Tm of 27.2 ± 0.3 °C. The inset shows the wild-type full-length mGlu5 data on a different scale. Data represent the mean ± s.d. from 3 independent experiments. b, mGlu5 crystallization construct (StaR(569–836)-T4L) in schematic representation. Thermostabilizing mutations (green) are: E579A, N667Y, I669A, G675M, T742A, S753A. Residues forming the allosteric pocket are pink. Disordered residues in the structure are grey. The disulphide bond between Cys6443.29–Cys733 is denoted by a dashed yellow line.

Extended Data Figure 2 Pharmacology of mGlu5StaR(569–836)-T4L.

Experiments performed in membranes from HEK293T cells transiently expressing mGlu5StaR(569–836)-T4L. a, Saturation binding of [3H]-M-MPEP to mGlu5StaR(569–836)-T4L. Non-specific binding was determined by addition of 0.1 mM MPEP. The data shown (mean ± s.e.m.) is representative of three independent experiments performed in duplicate. Data were fitted globally to a one-site saturation isotherm yielding a Kd of 0.86 ± 0.04 nM and Bmax of 54.7 ± 9.5 pmol mg−1. b, Competition binding. Membranes were incubated with varying concentrations (3 nM–10 µM) of the mGlu5 NAMs fenobam, dipraglurant, MPEP and mavoglurant. Inhibition curves were fitted to a four-parameter logistic equation to determine IC50 values, which were converted to Ki values using Kd values determined by saturation binding and the [3H]-M-MPEP concentration of 1 nM. The pKi values obtained are shown in Extended Data Table 2. Data shown are the mean ± s.e.m. of three independent experiments.

Extended Data Figure 3 Crystal packing in the mGlu5StaR(569–836)-T4L monoclinic C121 system.

a, View of the crystal lattice in the bc and ac planes respectively. The single copy of the mGlu5StaR(569–836)-T4L fusion present in the asymmetric unit is shown as Cα-trace (magenta). Symmetry mates shown as Cα-trace with the receptor TMD coloured green and T4L orange. mGlu5 receptor TMDs stack along the c axis in layers mediated by T4L. b, mGlu5 receptor TMDs pack through an interface mediated by antiparallel TM4–TM4 interactions with the T4L domain swung out towards one side of the receptor. c, The extracellular loops of the mGlu5 TMD are not constrained by packing interactions. Receptor and T4L coloured as in a. Two specific interactions are observed between the mGlu5-TMD N-terminal helical extension and T4L moiety from a symmetry mate. d, The intracellular loops of the mGlu5 TMD are not constrained by packing interactions, receptor and T4L coloured as in a. e, f, Result of 10 ns MD simulation on the mGlu5TMD, models shown are separated by 2 ns of simulation. Cα r.m.s.d. (between starting and final model) = 2.0 Å.

Extended Data Figure 4 T4L mediated contacts in the mGlu5StaR(569–836)-T4L monoclinic C121 system.

T4L layers are held together by extensive contacts between the T4L moieties. Specifically the N-terminal lobes of T4L (residues 1002–1071) are shifted by up to 3.7  (distance between equivalent Ca positions of E1022) in comparison to the input structure to molecular replacement and refinement (residues 1002-1071 from PDB ID: 3EML). The N-terminal lobes of T4L appear to pivot at V1071 to accommodate packing interactions in the mGlu5StaR(569–836)-T4L monoclinic C121 system, forming an intramolecular β-sheet between residues Y1018–K1019 and Y1018′–K1019′ of a symmetry mate, with additional hydrogen bonds between the back bone of G1012–L1013 and G1012′–L1013′. Hydrogen bonds denoted by dashed red lines, distances measured in angstroms.

Extended Data Figure 5 Constitutive activity of mGlu5 mutants.

IP1 response and number of receptors per cells in HEK293 cells transiently transfected to express wild-type (WT) or the indicated mGlu5 mutants. a, Constitutive activity of wild-type and mutant constructs expressed as percentage of background IP1 levels detected in mock transfected control sample. b, Numbers of expressed receptors per cell were determined using [3H]-M-MPEP binding. Error bars indicate standard error of mean and P values are derived from an unpaired two-tailed t-test. Data are representative of three independent experiments.

Extended Data Table 1 Comparison of the pharmacology of mGlu5 and mGlu5 StaR(569–836)-T4L
Extended Data Table 2 Data collection and refinement statistics for mGlu5StaR(569–836)-T4L
Extended Data Table 3 Representative alignment of 22 human class C receptor sequences (taken from an alignment of 156 class C receptor sequences)
Extended Data Table 4 Structural differences between mGlu5, class B and selected class A GPCRs
Extended Data Table 5 Alignment and comparison of allosteric binding site residues across the 8 human metabotropic glutamate receptors

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Doré, A., Okrasa, K., Patel, J. et al. Structure of class C GPCR metabotropic glutamate receptor 5 transmembrane domain. Nature 511, 557–562 (2014). https://doi.org/10.1038/nature13396

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