3GJN

Following evolutionary paths to high affinity and selectivity protein-protein interactions using Colicin7 and Immunity proteins


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Following evolutionary paths to protein-protein interactions with high affinity and selectivity

Levin, K.B.Dym, O.Albeck, S.Magdassi, S.Keeble, A.H.Kleanthous, C.Tawfik, D.S.

(2009) Nat Struct Mol Biol 16: 1049-1055

  • DOI: https://doi.org/10.1038/nsmb.1670
  • Primary Citation of Related Structures:  
    3GJN

  • PubMed Abstract: 

    How do intricate multi-residue features such as protein-protein interfaces evolve? To address this question, we evolved a new colicin-immunity binding interaction. We started with Im9, which inhibits its cognate DNase ColE9 at 10(-14) M affinity, and evolved it toward ColE7, which it inhibits promiscuously (Kd > 10(-8) M). Iterative rounds of random mutagenesis and selection toward higher affinity for ColE7, and selectivity (against ColE9 inhibition), led to an approximately 10(5)-fold increase in affinity and a 10(8)-fold increase in selectivity. Analysis of intermediates along the evolved variants revealed that changes in the binding configuration of the Im protein uncovered a latent set of interactions, thus providing the key to the rapid divergence of new Im7 variants. Overall, protein-protein interfaces seem to share the evolvability features of enzymes, that is, the exploitation of promiscuous interactions and alternative binding configurations via 'generalist' intermediates, and the key role of compensatory stabilizing mutations in facilitating the divergence of new functions.


  • Organizational Affiliation

    Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Colicin-E9 immunity protein
A, D
86Escherichia coliMutation(s): 7 
Gene Names: immceiE9
UniProt
Find proteins for P13479 (Escherichia coli)
Explore P13479 
Go to UniProtKB:  P13479
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13479
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Colicin-E7
B, C
141Escherichia coliMutation(s): 1 
Gene Names: colE7cea
EC: 3.1
UniProt
Find proteins for Q47112 (Escherichia coli)
Explore Q47112 
Go to UniProtKB:  Q47112
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47112
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.48 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.65α = 90
b = 53.713β = 105.59
c = 79.334γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-03-27
    Changes: Experimental preparation
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Refinement description