5MFI

Designed armadillo repeat protein YIII(Dq.V2)4CqI in complex with peptide (KR)4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Curvature of designed armadillo repeat proteins allows modular peptide binding.

Hansen, S.Ernst, P.Konig, S.L.B.Reichen, C.Ewald, C.Nettels, D.Mittl, P.R.E.Schuler, B.Pluckthun, A.

(2018) J. Struct. Biol. 201: 108-117

  • DOI: 10.1016/j.jsb.2017.08.009
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Designed armadillo repeat proteins (dArmRPs) were developed to create a modular peptide binding technology where each of the structural repeats binds two residues of the target peptide. An essential prerequisite for such a technology is a dArmRP geom ...

    Designed armadillo repeat proteins (dArmRPs) were developed to create a modular peptide binding technology where each of the structural repeats binds two residues of the target peptide. An essential prerequisite for such a technology is a dArmRP geometry that matches the peptide bond length. To this end, we determined a large set (n=27) of dArmRP X-ray structures, of which 12 were previously unpublished, to calculate curvature parameters that define their geometry. Our analysis shows that consensus dArmRPs exhibit curvatures close to the optimal range for modular peptide recognition. Binding of peptide ligands can induce a curvature within the desired range, as confirmed by single-molecule FRET experiments in solution. On the other hand, computationally designed ArmRPs, where side chains have been chosen with the intention to optimally fit into a geometrically optimized backbone, turned out to be more divergent in reality, and thus not suitable for continuous peptide binding. Furthermore, we show that the formation of a crystal lattice can induce small but significant deviations from the curvature adopted in solution, which can interfere with the evaluation of repeat protein scaffolds when high accuracy is required. This study corroborates the suitability of consensus dArmRPs as a scaffold for the development of modular peptide binders.


    Organizational Affiliation

    Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland.,Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zürich, Switzerland. Electronic address: plueckthun@bioc.uzh.ch.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YIII(Dq.V2)4CqI
A, B
243N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
(KR)4
C, D
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.800α = 90.00
b = 89.250β = 90.00
c = 107.500γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2018-02-21
    Type: Database references