5IVN

BC2 nanobody in complex with the BC2 peptide tag


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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

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

(2016) Sci Rep 6: 19211

  • DOI: 10.1038/srep19211
  • Primary Citation of Related Structures:  

  • 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 b ...

    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.


    Organizational Affiliation

    Interfaculty Institute of Biochemistry, Eberhard-Karls University Tuebingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BC2-nanobody
A
131N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cadherin derived peptide
B
12Homo sapiensMutation(s): 0 
Gene Names: CTNNB1
Find proteins for G9GAG7 (Homo sapiens)
Go to Gene View: CTNNB1
Go to UniProtKB:  G9GAG7
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
N7P
Query on N7P
B
L-peptide linkingC7 H11 N O3PRO
6E4
Query on 6E4
B
L-peptide linkingC5 H11 N3 O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.128 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.010α = 90.00
b = 31.530β = 107.54
c = 35.880γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2017-06-21
    Type: Derived calculations