The amino terminus of class II G protein-coupled receptors plays an important role in ligand binding and receptor activation. Understanding of the conformation of the amino-terminal domain of these receptors has been substantially advanced with the solution of nuclear magnetic resonance and crystal structures of this region of receptors for corticotrophin-releasing factor, pituitary adenylate cyclase-activating polypeptide, and gastric inhibitory polypeptide. However, the orientation of the amino terminus relative to the receptor core and how the receptor gets activated upon ligand binding remain unclear. In this work, we have used photoaffinity labeling to identify a critical spatial approximation between residue five of secretin and a residue within the proposed third extracellular loop of the secretin receptor.This was achieved by purification, deglycosylation, cyanogen bromide cleavage, and sequencing of labeled wild-type and mutant secretin receptors. This constraint has been used to refine our evolving molecular model of secretin docked at the intact receptor, which for the first time includes refined helical bundle and loop regions and reflects a peptide-binding groove within the receptor amino terminus that directs the amino terminus of the peptide toward the receptor body. This model is fully consistent with the endogenous agonist mechanism for class II G protein-coupled receptor activation, where ligand binding promotes the interaction of a portion of the receptor amino terminus with the receptor body to activate it.Class II guanine nucleotide-binding protein (G protein)-coupled receptors are an important family of potential drug targets that are activated by natural peptide ligands greater than 25 residues in length (Ulrich et al., 1998). All of these agonist ligands possess diffuse pharmacophoric regions, with critical residues spread throughout the length of the peptides. This provides the opportunity to define spatial approximation between such ligand residues and distinct residues within its receptor because ligand and receptor are normally bound to each other. It has been remarkable that probes incorporating photolabile residues throughout the pharmacophore of secretin-27, in positions 6, 12, 13, 14, 18, 21, 22, 23, and 26, each covalently labeled distinct residues that are restricted to the amino-terminal region of the secretin receptor, without labeling the receptor transmembrane core (Dong et al