PDBsum entry 5ivn

Peptide binding protein

PDB id: 5ivn

Contents

Protein chains

123 a.a.

12 a.a.

Waters ×134

PDB id:

5ivn

Name:

Peptide binding protein

Title:

Bc2 nanobody in complex with the bc2 peptide tag

Structure:

Bc2-nanobody. Chain: a. Engineered: yes. Cadherin derived peptide. Chain: b. Fragment: unp residues 16-27. Engineered: yes. Other_details: n7p is n-acetylated proline. 6e4 is amidated glutamin.

Source:

Vicugna pacos. Alpaca. Organism_taxid: 30538. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606

Resolution:

1.00Å R-factor: 0.129 R-free: 0.150

Authors:

M.B.Braun,T.Stehle

Key ref:

M.B.Braun et al. (2016). Peptides in headlock--a novel high-affinity and versatile peptide-binding nanobody for proteomics and microscopy. Sci Rep, 6, 19211. PubMed id: 26791954 DOI: 10.1038/srep19211

Date:

21-Mar-16 Release date: 06-Apr-16

Protein chain

No UniProt id for this chain

Struc: 123 a.a.

Protein chain

G9GAG7  (G9GAG7_HUMAN) -  Cadherin-associated protein (Fragment) from Homo sapiens

Seq: 71 a.a.

Struc: 12 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1038/srep19211

Sci Rep 6:19211 (2016)

PubMed id: 26791954

Peptides in headlock--a novel high-affinity and versatile peptide-binding nanobody for proteomics and microscopy.

M.B.Braun, B.Traenkle, P.A.Koch, F.Emele, F.Weiss, O.Poetz, T.Stehle, U.Rothbauer.

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.