All versions of PCIe are 100% backwards compatible, much like USB. Your device will run at the speed of the slowest part (in this case it'll run at PCIe 2.0 speeds). You could put that card in a PCIe 1.0 1x slot if you wanted and in theory it would still work.
By the way, you won't lose any performance from using PCIe 2.0 x 16 lanes, as no single GPU can utilise all the bandwidth of that. If you are using PCIe 2.0 x8 lanes slot, then you will lose a few FPS ~10%.