5IVN

BC2 nanobody in complex with the BC2 peptide tag


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1038/srep19211
  • Primary Citation of Related Structures:  
    5IVN, 5IVO

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BC2-nanobody131Vicugna pacosMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cadherin derived peptide12Homo sapiensMutation(s): 0 
UniProt
Find proteins for G9GAG7 (Homo sapiens)
Explore G9GAG7 
Go to UniProtKB:  G9GAG7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9GAG7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
N7P
Query on N7P
B
L-PEPTIDE LINKINGC7 H11 N O3PRO
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.00 Å
  • R-Value Free: 0.150 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.129 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.01α = 90
b = 31.53β = 107.54
c = 35.88γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2017-06-21
    Changes: Derived calculations
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description