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1 SUPPLEMENTARY INFORMATION doi: /nature22394 Supplementary Table 1 Observed intermolecular interactions within the GLP-1:GLP-1R TMD interface. Superscripts refer to the Wootten residue numbering system in which the single most conserved residue among class B GPCRs is designated X.50, where X is the transmembrane helix number. References regarding mutagenesis studies for each residue are listed. Residue in GLP-1 Residue in GLP-1R Reference His7 Glu9 R299 ECL2 1-3 W b 1-3 Y b 3,4 R b 4-8 L b 4,9,10 S b 6,10,11 Thr11 R299 ECL2 1-3 Phe12 Y b 3,4 F b 2,9,11,12 Thr13 K b 5,7,8,13-15 Ser14, Ser17, Ser18 (Serine Cluster) Leu20 Trp31 W297 ECL2 1,3 T298 ECL2 1 R299 ECL2 1-3 L b 9,16 M b 4 Q211 ECL1 4 H212 ECL
2 RESEARCH SUPPLEMENTARY INFORMATION Supplementary Table 2 Data collection and refinement statistics. Data collection/processing Voltage (kv) 300 Magnification 50,000 Defocus (µm) -1.5 to -3.0 Pixel size (Å) 1.0 Total electron dose (e - /Å 2 ) 90 Exposure time (s) 10 Number of images 17,332 Number of frames per image 50 Initial particle number 2,675,742 Particle number for 3D classification 620,626 Final particle number Resolution (core/global) (Å) 3.9/4.1 Map sharpened B-factor (Å 2 ) -350 Model refinement Non-hydrogen atoms 9099 R. M. S. Deviations Bond length (Å) Bond angle ( o ) Ramachandran plot Favored (%) 5.3 Allowed (%) 4.4 Outlier (%) 0.3 Rotamer outliers (%)
3 Supplemental Figure 1 Sequence alignment of GCGR subfamily GPCRs. SUPPLEMENTARY INFORMATION RESEARCH W W W. N A T U R E. C O M / N A T U R E 3
4 RESEARCH SUPPLEMENTARY INFORMATION 4 W W W. N A T U R E. C O M / N A T U R E
5 SUPPLEMENTARY INFORMATION RESEARCH Supplementary reference: 1 Koole, C. et al. Second extracellular loop of human glucagon-like peptide-1 receptor (GLP-1R) has a critical role in GLP-1 peptide binding and receptor activation. J. Biol. Chem. 287, (2012). 2 Dods, R. L. & Donnelly, D. The peptide agonist-binding site of the glucagon-like peptide-1 (GLP-1) receptor based on site-directed mutagenesis and knowledge-based modelling. Biosci. Rep. 36, e00285 (2015). 3 Yang, D. et al. Structural Determinants of Binding the Seven-transmembrane Domain of the Glucagon-like Peptide-1 Receptor (GLP-1R). J. Biol. Chem. 291, (2016). 4 Siu, F. Y. et al. Structure of the human glucagon class B G-protein-coupled receptor. Nature 499, (2013). 5 Yaqub, T. et al. Identification of determinants of glucose-dependent insulinotropic polypeptide receptor that interact with N-terminal biologically active region of the natural ligand. Mol. Pharmacol. 77, (2010). 6 Wootten, D., Simms, J., Miller, L. J., Christopoulos, A. & Sexton, P. M. Polar transmembrane interactions drive formation of ligand-specific and signal pathway-biased family B G protein-coupled receptor conformations. Proc. Natl. Acad. Sci. U. S. A. 110, (2013). 7 Coopman, K. et al. Residues within the transmembrane domain of the glucagon-like peptide-1 receptor involved in ligand binding and receptor activation: modelling the ligand-bound receptor. Mol. Endocrinol. 25, (2011). 8 Xiao, Q., Jeng, W. & Wheeler, M. B. Characterization of glucagon-like peptide-1 receptor-binding determinants. J. Mol. Endocrinol. 25, (2000). 9 Dong, M. et al. Mapping spatial approximations between the amino terminus of secretin and each of the extracellular loops of its receptor using cysteine trapping. FASEB J. 26, (2012). 10 Ceraudo, E. et al. Spatial proximity between the VPAC1 receptor and the amino terminus of agonist and antagonist peptides reveals distinct sites of interaction. FASEB J. 26, (2012). 11 Cascieri, M. A. et al. Characterization of a novel, non-peptidyl antagonist of the human glucagon receptor. J. Biol. Chem. 274, (1999). 12 Wootten, D. et al. The Extracellular Surface of the GLP-1 Receptor Is a Molecular Trigger for Biased Agonism. Cell 165, (2016). 13 Perret, J. et al. Mutational analysis of the glucagon receptor: similarities with the vasoactive intestinal peptide (VIP)/pituitary adenylate cyclase-activating peptide (PACAP)/secretin receptors for recognition of the ligand's third residue. Biochem. J. 362, (2002). 14 Di Paolo, E. et al. Contribution of the second transmembrane helix of the secretin receptor to the positioning of secretin. FEBS Lett. 424, (1998). 15 Solano, R. M. et al. Two basic residues of the h-vpac1 receptor second transmembrane helix are essential for ligand binding and signal transduction. J. Biol. Chem. 276, (2001). 16 Roberts, D. J., Vertongen, P. & Waelbroeck, M. Analysis of the glucagon receptor first extracellular loop by the substituted cysteine accessibility method. Peptides 32, (2011). 5
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