3Q9U

In silico and in vitro co-evolution of a high affinity complementary protein-protein interface


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A de novo protein binding pair by computational design and directed evolution.

Karanicolas, J.Corn, J.E.Chen, I.Joachimiak, L.A.Dym, O.Peck, S.H.Albeck, S.Unger, T.Hu, W.Liu, G.Delbecq, S.Montelione, G.T.Spiegel, C.P.Liu, D.R.Baker, D.

(2011) Mol Cell 42: 250-260

  • DOI: https://doi.org/10.1016/j.molcel.2011.03.010
  • Primary Citation of Related Structures:  
    3Q9N, 3Q9U, 3QA9

  • PubMed Abstract: 

    The de novo design of protein-protein interfaces is a stringent test of our understanding of the principles underlying protein-protein interactions and would enable unique approaches to biological and medical challenges. Here we describe a motif-based method to computationally design protein-protein complexes with native-like interface composition and interaction density. Using this method we designed a pair of proteins, Prb and Pdar, that heterodimerize with a Kd of 130 nM, 1000-fold tighter than any previously designed de novo protein-protein complex. Directed evolution identified two point mutations that improve affinity to 180 pM. Crystal structures of an affinity-matured complex reveal binding is entirely through the designed interface residues. Surprisingly, in the in vitro evolved complex one of the partners is rotated 180° relative to the original design model, yet still maintains the central computationally designed hotspot interaction and preserves the character of many peripheral interactions. This work demonstrates that high-affinity protein interfaces can be created by designing complementary interaction surfaces on two noninteracting partners and underscores remaining challenges.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195-7350, USA. johnk@ku.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CoA binding protein
A, B
141Escherichia coliMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
consensus ankyrin repeat
C, D
158Escherichia coliMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
COA Binding MOAD:  3Q9U Kd: 130 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.244 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.901α = 89.96
b = 57.62β = 90.14
c = 58.23γ = 113.44
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-07-20
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description