The development of multivalent protein ligands for nanoparticles lags behind that of multidentate polymer and small molecule ligands, largely because of a lack of thorough understanding on the interaction between nanoparticles and multimeric proteins. Guided by protein crystal structures, we have harnessed recombinant technology to develop a collection of mCherry fused multimeric proteins with different spatial distribution of quantum dot (QD)-binding sequence, hexahistidine tag (histag). All the proteins can behave as ligands to assemble with ZnS-CdSe QDs through metal-affinity driven self-assembly. We have observed that protein shape and geometry greatly affect the stoichiometry and stability of their assemblies with QDs. We also demonstrate a peptide-induced structural transition of a nanobelt protein that pre-organizes the QD-binding sites and effects a more efficient assembly with QDs. This work reports the first multifaceted investigation on how multivalent proteins, in particular dimer, tetramers and linear multidentate proteins, assemble with QDs. It also manifests our capability of harnessing the structural and conformational information of proteins to design multivalent protein ligands for QD surface functionalization.