The professional animator and molecular biologist Janet Iwasa at Harvard Medical School is generating beautiful animations of cellular processes such as proteasome structure and function or endocytosis. Importantly, she has published these on her website with a Creative Commons license so that everyone has access to them. She has been interviewed by EarthSky, where she explains why she became a molecular animator.
Movie about the proteasome structure:
http://iwasa.hms.harvard.edu/project_pages/proteasome/downloads/proteasome_structure.mov
Movie about chromosome segregation:
https://iwasa.hms.harvard.edu/project_pages/CIN/downloads/normal.mov
Movie about protein translocation (movement of proteins across membranes):
There are plenty of other beautiful animations and illustrations on her website and I highly recommend that anyone with an interest in cell biology should explore those.
The Next Regeneration 