3QA9

Crystal Structure of Prb (PH1109 protein redesigned for binding)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.molcel.2011.03.010
  • Primary Citation of Related Structures:  

  • 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-base ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CoA binding domain protein
A
149N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.003α = 90.00
b = 59.395β = 90.00
c = 60.038γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata scaling
CrystalCleardata collection
d*TREKdata reduction
CNSrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-01-10 
  • Released Date: 2011-04-20 
  • Deposition Author(s): Spiegel, P.C.

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-07-20
    Type: Database references