The skull was removed by Francisco de Orellana and stayed with him in the tomb.
It was the obsession of Harold Oxley, who heavily researched the connection of the Skull to a Peruvian legend about a City of Gold.
Powers and Physical Makeup
The Skull is incredibly magnetic, even attracting metals that aren't by nature magnetic themselves like gold. The Skull also has psychic abilities, being able to communicate on a primitive level with other creatures by staring into the eyes for prolonged periods. These powers also seem to have effect on non-humans such as the fire-ants that Indy and crew encounter that are repelled by the power emitted by the Skull.
Behind the scenes
It serves as the title McGuffin at the heart of Indiana Jones and the Kingdom of the Crystal Skull.