Owing to their influence on electrons and phonons, defects can significantly alter electrical conductance, and optical, mechanical and thermal properties of a material. Thus, understanding and control of defects, including dopants in low-dimensional systems, hold great promise for engineered materials and nanoscale devices. Here, we characterize experimentally the effects of a single defect on electrons and phonons in single-wall carbon nanotubes. The effects demonstrated here are unusual in that they are not caused by defect-induced symmetry breaking. Electrons and phonons are strongly coupled in sp(2) carbon systems, and a defect causes renormalization of electron and phonon energies. We find that near a negatively charged defect, the electron velocity is increased, which in turn influences lattice vibrations locally. Combining measurements on nanotube ensembles and on single nanotubes, we capture the relation between atomic response and the readily accessible macroscopic behaviour.