CRAC channels generate Ca 2؉ signals critical for the activation of immune cells and exhibit an intriguing pore profile distinguished by extremely high Ca 2؉ selectivity, low Cs ؉ permeability, and small unitary conductance. To identify the ion conduction pathway and gain insight into the structural bases of these permeation characteristics, we introduced cysteine residues in the CRAC channel pore subunit, Orai1, and probed their accessibility to various thiolreactive reagents. Our results indicate that the architecture of the ion conduction pathway is characterized by a flexible outer vestibule formed by the TM1-TM2 loop, which leads to a narrow pore flanked by residues of a helical TM1 segment. Residues in TM3, and specifically, E190, a residue considered important for ion selectivity, are not close to the pore. Moreover, the outer vestibule does not significantly contribute to ion selectivity, implying that Ca 2؉ selectivity is conferred mainly by E106. The ion conduction pathway is sufficiently narrow along much of its length to permit stable coordination of Cd 2؉ by several TM1 residues, which likely explains the slow flux of ions within the restrained geometry of the pore. These results provide a structural framework to understand the unique permeation properties of CRAC channels.Orai1 ͉ STIM1 ͉ store-operated channels C a 2ϩ release-activated Ca 2ϩ (CRAC) channels are the principal route of Ca 2ϩ entry in immune cells and orchestrate functions such as gene expression, motility, and the release of inflammatory mediators (1). Mutations in CRAC channels give rise to devastating immunodeficiencies and abnormalities in muscle, skin, and teeth, highlighting their importance for various organ systems (1). The recent discoveries of STIM1 (the ER Ca 2ϩ sensor), and Orai1 (the CRAC channel pore subunit) have provided major breakthroughs to illuminate the molecular basis of CRAC channel function (2). However, while the identification of these proteins has produced rapid progress in our understanding of the cellular events underlying channel activation, the molecular mechanisms of ion selectivity and permeation remain unclear.CRAC channels are distinguished by an extraordinarily high selectivity for Ca 2ϩ over monovalent ions (P Ca /P Na Ͼ 1,000), a very low unitary conductance (Ͻ1 pS), and low permeability to Cs ϩ and larger monovalent cations (3). The structural underpinnings of these characteristics have been the focus of much debate but are largely unknown. As with most ion channels, the pore properties of CRAC channels are likely shaped by the arrangement and chemistry of pore-lining residues. Thus, to understand the basis of the unique permeation properties of CRAC channels, the residues lining the ion transport pathway need to be elucidated.Orai1 bears little sequence homology to other ion channel proteins, and consequently, there are few clues regarding the contribution of the different parts of the molecule for pore formation. Electrophysiological studies indicate that the exquisite Ca 2ϩ selectivity of CRAC...