6NUK

De novo designed protein Ferredog-Diesel


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

De novo protein design by citizen scientists.

Koepnick, B.Flatten, J.Husain, T.Ford, A.Silva, D.A.Bick, M.J.Bauer, A.Liu, G.Ishida, Y.Boykov, A.Estep, R.D.Kleinfelter, S.Norgard-Solano, T.Wei, L.Players, F.Montelione, G.T.DiMaio, F.Popovic, Z.Khatib, F.Cooper, S.Baker, D.

(2019) Nature 570: 390-394

  • DOI: 10.1038/s41586-019-1274-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Online citizen science projects such as GalaxyZoo <sup>1 </sup>, Eyewire <sup>2 </sup> and Phylo <sup>3 </sup> have proven very successful for data collection, annotation and processing, but for the most part have harnessed human pattern-recognition ...

    Online citizen science projects such as GalaxyZoo 1 , Eyewire 2 and Phylo 3 have proven very successful for data collection, annotation and processing, but for the most part have harnessed human pattern-recognition skills rather than human creativity. An exception is the game EteRNA 4 , in which game players learn to build new RNA structures by exploring the discrete two-dimensional space of Watson-Crick base pairing possibilities. Building new proteins, however, is a more challenging task to present in a game, as both the representation and evaluation of a protein structure are intrinsically three-dimensional. We posed the challenge of de novo protein design in the online protein-folding game Foldit 5 . Players were presented with a fully extended peptide chain and challenged to craft a folded protein structure and an amino acid sequence encoding that structure. After many iterations of player design, analysis of the top-scoring solutions and subsequent game improvement, Foldit players can now-starting from an extended polypeptide chain-generate a diversity of protein structures and sequences that encode them in silico. One hundred forty-six Foldit player designs with sequences unrelated to naturally occurring proteins were encoded in synthetic genes; 56 were found to be expressed and soluble in Escherichia coli, and to adopt stable monomeric folded structures in solution. The diversity of these structures is unprecedented in de novo protein design, representing 20 different folds-including a new fold not observed in natural proteins. High-resolution structures were determined for four of the designs, and are nearly identical to the player models. This work makes explicit the considerable implicit knowledge that contributes to success in de novo protein design, and shows that citizen scientists can discover creative new solutions to outstanding scientific challenges such as the protein design problem.


    Organizational Affiliation

    Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.,Department of Biochemistry, University of Washington, Seattle, WA, USA.,Institute for Protein Design, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,Nexomics Biosciences, Bordentown, NJ, USA.,Department of Biochemistry, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA, USA.,Institute for Protein Design, University of Washington, Seattle, WA, USA.,Department of Molecular Biology and Biochemistry, Rutgers University The State University of New Jersey, Piscataway, NJ, USA.,Center for Game Science, Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.,Department of Biochemistry, University of Washington, Seattle, WA, USA. dabaker@uw.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferredog-Diesel
A, B
104N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.248 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.210α = 90.00
b = 69.210β = 90.00
c = 90.590γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical InstituteUnited States--
National Science Foundation (United States)United StatesDGE-1256082

Revision History 

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-06-19
    Type: Data collection, Database references
  • Version 1.2: 2019-07-03
    Type: Data collection, Database references