Problem using Rotation in Show
myBox = Cuboid[{-40, 40, 0}, {40, 60, 10}];
Show@MapAt[Rotate[#, Pi/4, {0, 0, 1}, {0, 0, 0}] &, Graphics3D[myBox], {1}]
Manipulate[Table[Show[Graphics3D[{Red, Sphere[{0, 0, 0}, 30],
Green, Cylinder[{{30, 30, 30}, {40, 50, 40}}, 30]}],
MapAt[Rotate[#, k, v, {0, 0, 0}] &, Graphics3D[myBox], {1}],
Boxed -> False, PlotRange -> {{-100, 100}, {-100, 100}, {-100, 100}}],
{k, 0, 2 Pi, Pi/12}] // ListAnimate,
{{v, {1, 0, 0}}, {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}}}]