An atom has a tiny, positively charged nucleus with negatively charged electrons in orbit around it. The nucleus contains protons (positive) and neutrons (no charge), and it holds nearly all the mass of the atom.
The evidence comes from firing alpha particles at thin gold foil. Most went straight through, so the atom is mostly empty space. A few were deflected, and a very small number came back, so there must be a small, massive, positive centre repelling them.
The proton number fixes which element it is. Isotopes are atoms of the same element with different numbers of neutrons. A neutral atom has equal numbers of protons and electrons, and becomes an ion when it loses or gains electrons.