Current understanding of the brittleness of glass is limited by our poor understanding and control over the microscopic structure. In this study, we used a pressure quenching route to tune the structure of silica glass in a controllable manner, and observed a systematic increase in ductility in samples quenched under increasingly higher pressure. The brittle to ductile transition in densified silica glass can be attributed to the critical role of 5-fold Si coordination defects (bonded to 5 O neighbors) in facilitating shear deformation and in dissipating energy by converting back to the 4-fold coordination state during deformation. As an archetypal glass former and one of the most abundant minerals in the Earth's crest, a fundamental understanding of the microscopic structure underpinning the ductility of silica glass will not only pave the way toward rational design of strong glasses, but also advance our knowledge of the geological processes in the Earth's interior.