After receiving her doctorate, she worked at the University of California, San Francisco, from 2003 to 2009 as a Damon Runyon and Burroughs Wellcome Career Award postdoctoral fellow with Ron Vale. There, Antonina Roll-Mecak identified spastin as a novel microtubule-severing enzyme and used hybrid structural biology methods and light microscopy to reveal the first three dimensional structure of a microtubule severing enzyme and to unravel its mechanism of action. Her analyses led to the proposal that severing enzymes break the microtubule by pulling single tubulin dimers out of the microtubule lattice.