We report on the investigation of the atomic and electronic structures of a clean Si(331)-(12 × 1) surface using a first-principles approach with both plane wave and strictly localized basis sets. Starting from the surface structure proposed by Zhachuk and Teys [Phys. Rev. B 95, 041412(R) (2017)], we develop significant improvements to the atomic model and localized basis set which are critical for the correct description of the observed bias dependence of scanning tunneling microscopy (STM) images. The size mismatch between the Si pentamers from the surface model and those seen by STM is explained within the context of the Tersoff-Hamann model. The energy barriers that separate different Si(331) buckled configurations were estimated, showing that the surface structure is prone to dynamic buckling at room temperature. It is found that empty electronic states on Si(331) are essentially localized on the pentamers with interstitials and under-coordinated Si sp 2-like atoms between them, while filled electronic states are localized on under-coordinated Si sp 3-like atoms and dimers on trenches. The calculated electronic density of states exhibits two broad peaks in the fundamental bandgap of Si: one near the valence band top and the other near the conduction band bottom. The resulting surface bandgap of 0.58 eV is in an excellent agreement with spectroscopy studies.