I think that your brother is a clever boy.
I(主) think(谓) that your brother is a clever boy (that引导的从句为think的宾语,that在从句中不做成分).
your brother(从句主语) is(从句系动词) a clever boy(从句表语,亦可理解为从句主语的表语——对从句主语your brother进行补充)