3Q9N

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 

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 protein
A, B
141N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
consensus ankyrin repeat
C, D
158N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CMS
Query on CMS

Download SDF File 
Download CCD File 
A
CARBAMOYL SARCOSINE
C4 H8 N2 O3
SREKYKXYSQMOIB-UHFFFAOYSA-N
 Ligand Interaction
COA
Query on COA

Download SDF File 
Download CCD File 
A, B
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
COAKd: 130 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 53.122α = 89.78
b = 56.556β = 112.42
c = 56.977γ = 90.03
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHENIXrefinement
HKL-2000data collection
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2011-04-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-07-20
    Type: Database references