Atoms have two main parts: a massive nucleus at the center and a swarm of fast-moving electrons around it. The nucleus is made up of protons and (usually) neutrons. Almost all of the mass (more than 99%) of an atom is in the dense nucleus.
An atomic nucleus is much, much smaller than an atom. The cloud of electrons that "orbit" the nucleus and define the "size" of an atom is about 100,000 times as large as that atom's nucleus! If you made a scale model of an atom with a nucleus the size of a pea, the electrons would zing around in a space larger than a major sports stadium! An atom is mostly empty space.