5IVN

BC2 nanobody in complex with the BC2 peptide tag

Summary for 5IVN

• Entry DOI: 10.2210/pdb5ivn/pdb
• Descriptor: BC2-nanobody, Cadherin derived peptide (3 entities in total)
• Functional Keywords: nanobody, tag, capture, affinity, catenin, peptide binding protein
• Biological source: Vicugna pacos (Alpaca); More
• Total number of polymer chains: 2
• Total formula weight: 16200.91

Authors

Braun, M.B.,Stehle, T. (deposition date: 2016-03-21, release date: 2016-04-06, Last modification date: 2024-01-10)

Primary citation

Braun, M.B.,Traenkle, B.,Koch, P.A.,Emele, F.,Weiss, F.,Poetz, O.,Stehle, T.,Rothbauer, U.
Peptides in headlock - a novel high-affinity and versatile peptide-binding nanobody for proteomics and microscopy.
Sci Rep, 6:19211-, 2016

PubMed Abstract: Nanobodies are highly valuable tools for numerous bioanalytical and biotechnical applications. Here, we report the characterization of a nanobody that binds a short peptide epitope with extraordinary affinity. Structural analysis reveals an unusual binding mode where the extended peptide becomes part of a β-sheet structure in the nanobody. This interaction relies on sequence-independent backbone interactions augmented by a small number of specificity-determining side chain contacts. Once bound, the peptide is fastened by two nanobody side chains that clamp it in a headlock fashion. Exploiting this unusual binding mode, we generated a novel nanobody-derived capture and detection system. Matrix-coupled nanobody enables the fast and efficient isolation of epitope-tagged proteins from prokaryotic and eukaryotic expression systems. Additionally, the fluorescently labeled nanobody visualizes subcellular structures in different cellular compartments. The high-affinity-binding and modifiable peptide tag of this system renders it a versatile and robust tool to combine biochemical analysis with microscopic studies.

PubMed: 26791954
DOI: 10.1038/srep19211

Experimental method

X-RAY DIFFRACTION (1 Å)