The crystal structure of PDZ-Fibronectin fusion protein

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 

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Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution.

Huang, J.Makabe, K.Biancalana, M.Koide, A.Koide, S.

(2009) J Mol Biol 392: 1221-1231

  • DOI: https://doi.org/10.1016/j.jmb.2009.07.067
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    We have established a new protein-engineering strategy termed "directed domain-interface evolution" that generates a binding site by linking two protein domains and then optimizing the interface between them. Using this strategy, we have generated synthetic two-domain "affinity clamps" using PDZ and fibronectin type III (FN3) domains as the building blocks. While these affinity clamps all had significantly higher affinity toward a target peptide than the underlying PDZ domain, two distinct types of affinity clamps were found in terms of target specificity. One type conserved the specificity of the parent PDZ domain, and the other increased the specificity dramatically. Here, we characterized their specificity profiles using peptide phage-display libraries and scanning mutagenesis, which suggested a significantly enlarged recognition site of the high-specificity affinity clamps. The crystal structure of a high-specificity affinity clamp showed extensive contacts with a portion of the peptide ligand that is not recognized by the parent PDZ domain, thus rationalizing the improvement of the specificity of the affinity clamp. A comparison with another affinity clamp structure showed that, although both had extensive contacts between PDZ and FN3 domains, they exhibited a large offset in the relative position of the two domains. Our results indicate that linked domains could rapidly fuse and evolve as a single functional module, and that the inherent plasticity of domain interfaces allows for the generation of diverse active-site topography. These attributes of directed domain-interface evolution provide facile means to generate synthetic proteins with a broad range of functions.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
fusion protein PDZ-Fibronectin,Fibronectin195Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RT1 (Homo sapiens)
Explore Q96RT1 
Go to UniProtKB:  Q96RT1
GTEx:  ENSG00000112851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96RT1
Sequence Annotations
  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
C-terminal octapeptide from protein ARVCFB [auth P]8synthetic constructMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.204 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.008α = 90
b = 69.008β = 90
c = 46.706γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Source and taxonomy, Structure summary