5IVN image
Entry Detail
PDB ID:
5IVN
Title:
BC2 nanobody in complex with the BC2 peptide tag
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2016-03-21
Release Date:
2016-04-06
Method Details:
Experimental Method:
Resolution:
1.00 Å
R-Value Free:
0.14
R-Value Work:
0.12
R-Value Observed:
0.12
Space Group:
C 1 2 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:BC2-nanobody
Chain IDs:A
Chain Length:131
Number of Molecules:1
Biological Source:Vicugna pacos
Polymer Type:polypeptide(L)
Description:Cadherin derived peptide
Chain IDs:B
Chain Length:12
Number of Molecules:1
Biological Source:Homo sapiens
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
6E4 B GLN modified residue
N7P B PRO modified residue
Primary Citation
Peptides in headlock - a novel high-affinity and versatile peptide-binding nanobody for proteomics and microscopy.
Sci Rep 6 19211 ? (2016)
PMID: 26791954 DOI: 10.1038/srep19211

Abstact

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.

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Primary Citation of related structures