Although the CA3-CA1 synapse is critically important for learning and memory, experimental limitations have to date prevented direct determination of the structural features that determine the response plasticity. Specifically, the local calcium influx responsible for vesicular release and short-term synaptic facilitation strongly depends on the distance between the voltage-dependent calcium channels (VDCCs) and the presynaptic active zone. Estimates for this distance range over two orders of magnitude. Here, we use a biophysically detailed computational model of the presynaptic bouton and demonstrate that available experimental data provide sufficient constraints to uniquely reconstruct the presynaptic architecture. We predict that for a typical CA3-CA1 synapse, there are ∼70 VDCCs located 300 nm from the active zone. This result is surprising, because structural studies on other synapses in the hippocampus report much tighter spatial coupling. We demonstrate that the unusual structure of this synapse reflects its functional role in short-term plasticity (STP).synaptic depression | paired-pulse facilitation | vesicle | MCell S ynaptic transmission is determined by the local calcium signal detected at the active zone, the actual locus of neurotransmitter release (1-3). Current experimental techniques can only measure the global calcium signal in a synaptic bouton. However, diffusion of calcium between its sources and sinks at the active zone, means that the local calcium concentration may be very different from the averaged global concentration. This concentration is transient and determined by the number of presynaptic voltage-dependent calcium channels (VDCCs), the main source of calcium, the distance between them and the active zone, and the calcium buffers and pumps in the terminal, the main sinks of calcium. The spatiotemporal properties of this calcium signal finely orchestrate many aspects of synaptic plasticity; hence these depend critically on the architectural features. Here we describe a unique computational approach that uses measurable quantities as modeling constraints and thus can compensate for the lack of direct structural evidence. In this manner, the model answers a key question in synaptic neurophysiology, namely, what is the number and geometry of the calcium channels at the CA3-CA1 synapse, crucial in learning and memory.Pharmacological and electrophysiological experiments at different synapses have reached different conclusions regarding presynaptic architecture. The frog neuromuscular junction, mouse hair cell ribbon synapse, and squid giant synapse all require only a small number of channels placed close to the release sites for vesicle fusion (4-8). In contrast, tens of channels are said to control fusion in the calyx of Held and cerebellar synapses (9-11). For small GABAergic synapses in the hippocampus, recent studies (12, 13) show that calcium channels and the active zone share a tight geometrical arrangement. This feature is argued to be essential for fast, efficient, and reliable s...