5GS2

Crystal structure of diabody complex with repebody and MBP

Summary for 5GS2

• Entry DOI: 10.2210/pdb5gs2/pdb
• Related: 5GRU 5GRV 5GRW 5GRX 5GRY 5GRZ 5GS0 5GS1 5GS3
• Descriptor: Maltose-binding periplasmic protein, anti-repebody, anti-MBP, ... (4 entities in total)
• Functional Keywords: diabody, antibody fragment, complex, sugar binding protein-immune system complex, sugar binding protein/immune system
• Biological source: Escherichia coli (strain K12); More
• Cellular location: Periplasm: P0AEX9
• Total number of polymer chains: 4
• Total formula weight: 121805.50

Authors

Kim, J.H.,Song, D.H.,Youn, S.J.,Kim, J.W.,Cho, G.,Lee, H.,Lee, J.O. (deposition date: 2016-08-13, release date: 2016-10-12, Last modification date: 2024-11-13)

Primary citation

Kim, J.H.,Song, D.H.,Youn, S.J.,Kim, J.W.,Cho, G.,Kim, S.C.,Lee, H.,Jin, M.S.,Lee, J.O.
Crystal structure of mono- and bi-specific diabodies and reduction of their structural flexibility by introduction of disulfide bridges at the Fv interface.
Sci Rep, 6:34515-34515, 2016

PubMed Abstract: Building a sophisticated protein nano-assembly requires a method for linking protein components in a predictable and stable structure. Diabodies are engineered antibody fragments that are composed of two Fv domains connected by short peptide linkers. They are attractive candidates for mediators in assembling protein nano-structures because they can simultaneously bind to two different proteins and are rigid enough to be crystallized. However, comparison of previous crystal structures demonstrates that there is substantial structural diversity in the Fv interface region of diabodies and, therefore, reliable prediction of its structure is not trivial. Here, we present the crystal structures of ten mono- and bi-specific diabodies. We found that changing an arginine residue in the Fv interface to threonine greatly reduced the structural diversity of diabodies. We also found that one of the bispecific diabodies underwent an unexpected process of chain swapping yielding a non-functional monospecific diabody. In order to further reduce structural flexibility and prevent chain shuffling, we introduced disulfide bridges in the Fv interface regions. The disulfide-bridged diabodies have rigid and predictable structures and may have applications in crystallizing proteins, analyzing cryo-electron microscopic images and building protein nano-assemblies.

PubMed: 27682821
DOI: 10.1038/srep34515

Experimental method

X-RAY DIFFRACTION (3.592 Å)