I think you are mixed up. GDDR5 is the memory on video cards and the video card itself uses a PCIE slot. GDDR3 is also on video cards and use PCIE Slots. They are all backwards compatible down to PCIE 16x 1.1 if you happen to own a computer from 2005.
You are asking if a video card with GDDR5 PCIE 3.0 card will work in a slot that had a video in it that was GDDR3 and PCIE 2.0. The answer is yes it will work.