6WVS

Hyperstable de novo TIM barrel variant DeNovoTIM15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Tight and specific lanthanide binding in a de novo TIM barrel with a large internal cavity designed by symmetric domain fusion.

Caldwell, S.J.Haydon, I.C.Piperidou, N.Huang, P.S.Bick, M.J.Sjostrom, H.S.Hilvert, D.Baker, D.Zeymer, C.

(2020) Proc Natl Acad Sci U S A 117: 30362-30369

  • DOI: https://doi.org/10.1073/pnas.2008535117
  • Primary Citation of Related Structures:  
    6WVS, 6WXO, 6WXP, 6ZV9

  • PubMed Abstract: 

    De novo protein design has succeeded in generating a large variety of globular proteins, but the construction of protein scaffolds with cavities that could accommodate large signaling molecules, cofactors, and substrates remains an outstanding challenge. The long, often flexible loops that form such cavities in many natural proteins are difficult to precisely program and thus challenging for computational protein design. Here we describe an alternative approach to this problem. We fused two stable proteins with C2 symmetry-a de novo designed dimeric ferredoxin fold and a de novo designed TIM barrel-such that their symmetry axes are aligned to create scaffolds with large cavities that can serve as binding pockets or enzymatic reaction chambers. The crystal structures of two such designs confirm the presence of a 420 cubic Ångström chamber defined by the top of the designed TIM barrel and the bottom of the ferredoxin dimer. We functionalized the scaffold by installing a metal-binding site consisting of four glutamate residues close to the symmetry axis. The protein binds lanthanide ions with very high affinity as demonstrated by tryptophan-enhanced terbium luminescence. This approach can be extended to other metals and cofactors, making this scaffold a modular platform for the design of binding proteins and biocatalysts.


  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, WA 98195.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DeNovoTIM15 hyperstable de novo TIM barrel193synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.203 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.199α = 90
b = 53.199β = 90
c = 64.27γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
PHASERphasing
Cootmodel building
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Defense Threat Reduction Agency (DTRA)United StatesHDTRA1-19-1-0003

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2020-12-02
    Changes: Database references, Structure summary
  • Version 1.2: 2020-12-16
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references