The problem of bacterial resistance has been recently brought to light due to the extra medical expenses and deaths involved in infections by resistant strains. Although there have been improvements in developing antimicrobials, the basic understanding of the mechanisms conferring resistance to Gram-negative bacteria is still needed to combat complex drug resistance. Among bacterial defense mechanisms, the efflux of antimicrobials by multi-drug and metal ion membrane pumps is the major concern in this dissertation. Particularly, the resistance-nodulation-cell division (RND) family has shown the power of bypassing the periplasm when pumping toxins and enhancing the efficacy of substrate extrusion. Drug resistance is also mediated at the genetic level by local repressors such as the TetR protein family. CmeR, a member of the TetR family from Campylobactor jejuni, represses the expression of the RND efflux pump CmeABC by binding at the promoter region of the cmeABC operon. CmeR has the ability to accommodate large amphiphiles. The crystal structures of the CmeR-bile acid complexes are presented to show the details of the ligand-binding tunnel at the C-terminal. In this dissertation, two other RND efflux systems, Cus and Mtr, are discussed. The importance of the first cysteine residue on the outer membrane protein CusC has been demonstrated by the crystal structures. The structures of the Cys1-mutated CusC suggest a possible route of the channel formation on the outer membrane prior to the assembly of the Cus efflux system. The efficient extrusion of antimicrobials requires an open state of the outer membrane channel in the RND efflux system. Recently, the crystal structure of MtrE, an outer membrane channel of the Mtr system from Neisseria gonorrhoeae, has also been solved. Due to the relaxed coiled-coils of the α -helical domain, the crystal structure of MtrE is found at its open state. The structural analysis of MtrE gives insights of a native open state of an outer membrane channel. In comparison with other outer membrane channels with known crystal structures, the structure of MtrE agrees with the transition theory hypothesized by the structure of TolC, the outer membrane channel of the AcrAB-TolC efflux system. In depth, the findings regarding RND-type efflux pumps and their transcriptional regulators should elucidate the mechanisms mediating drug resistance in bacteria at the atomic level.