We report a combined electronic transport and structural characterization study of small carbon nanotube bundles in field-effect transistors (FET). The atomic structures of the bundles are determined by electron diffraction using an observation window built in the FET. The single-walled nanotube bundles exhibit electrical transport characteristics sensitively dependent on the structure of individual tubes, their arrangements in the bundle, deformation due to intertube interaction, and the orientation with respect to the gate electric field. Our ab-initio simulation shows that tube deformation in the bundle induces a bandgap opening in a metallic tube. These results show the importance of intertube interaction in electrical transport of bundled nanotubes.