He looks purebred to me, although something about his face reminds me of a Malinois. But there's a great deal of individual differences between GSDs, and he probably is purebred. He looks like a sweet boy and I love his color. Do you know how old he is?
Yeah, he seems larger than 40 lb looking at his photo, but if he's a year and half old at that weight, it may be he has some Malinois, Tervuren or Belgian Shepherd . The shyness and skittish behavior is not uncommon in all those breeds. Take it slow and easy with him, treat him gently and with lots of patience. He's likely gone through a traumatic time at the shelter. After he settles in a bit, look into joining a basic obedience class with him.
He looks like gsd x dutch shep to me. But they aren't that small either. My german shepherd is pure bred and extremely small. We thought something was medically wrong she is so small. I would guess she won't make it to 40 pounds full grown. So anything is possible. Enjoy your new dog!