Pentameric ligand-gated ion channels mediate fast chemical transmission of nerve signals. The structure of a bacterial proton-gated homolog has been established in its open and locally closed conformations at acidic pH. We will report a new crystal structure at neutral pH, thereby providing the X-ray structures of the two end-points of the gating mechanism in the same pentameric ligand-gated ion channel. The large structural variability in the neutral pH structure observed in the four copies of the pentamer present in the asymmetric unit has been used to analyze the intrinsic fluctuations in this state, which are found to prefigure the transition to the open state. In the extracellular domain (ECD), a marked quaternary change is observed, involving both a twist and a blooming motion, and the pore in the transmembrane domain (TMD) is closed by an upper bend of helix M2 (as in locally closed form) and a kink of helix M1, both helices no longer interacting across adjacent subunits. On the tertiary level, detachment of inner and outer β sheets in the ECD reshapes two essential cavities at the ECD–ECD and ECD–TMD interfaces. As described with classical allosteric proteins, the tertiary changes of the subunits are linked together through the quaternary constraint by a marked reorganization of the interfaces between subunits and the associated binding pockets and cavities. The closed form displays a cavity that may allow a better understanding of the mechanism of action of pharmacological effectors of pentameric ligand-gated ion channels and the rational design of new modulators