The atomic nucleus is made of protons and neutrons (nucleons), that are themselves composed of quarks and gluons. Understanding how the quark-gluon structure of a nucleon bound in an atomic nucleus is modified by the surrounding nucleons is an outstanding challenge. Although evidence for such modification, known as the EMC effect, was first observed over 35 years ago, there is still no generally accepted explanation of its cause. Recent observations suggest that the EMC effect is related to close-proximity Short Range Correlated (SRC) nucleon pairs in nuclei. Here we report the first simultaneous, high-precision, measurements of the EMC effect and SRC abundances. We show that the EMC data can be explained by a universal modification of the structure of nucleons in neutron-proton (np) SRC pairs and present the first data-driven extraction of this universal modification function. This implies that, in heavier nuclei with many more neutrons than protons, each proton is more likely than each neutron to belong to an SRC pair and hence to have its quark structure distorted.