4ZV6

Crystal structure of the artificial alpharep-7 octarellinV.1 complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

The unexpected structure of the designed protein Octarellin V.1 forms a challenge for protein structure prediction tools.

Figueroa, M., Sleutel, M., Vandevenne, M., Parvizi, G., Attout, S., Jacquin, O., Vandenameele, J., Fischer, A.W., Damblon, C., Goormaghtigh, E., Valerio-Lepiniec, M., Urvoas, A., Durand, D., Pardon, E., Steyaert, J., Minard, P., Maes, D., Meiler, J., Matagne, A., Martial, J.A., Van de Weerdt, C.

(2016) J Struct Biol 195: 19-30

  • DOI: 10.1016/j.jsb.2016.05.004
  • Primary Citation of Related Structures:  
    4ZV6, 5BOP

  • PubMed Abstract: 

    • Despite impressive successes in protein design, designing a well-folded protein of more 100 amino acids de novo remains a formidable challenge. Exploiting the promising biophysical features of the artificial protein Octarellin V, we improved this protein ...

    Despite impressive successes in protein design, designing a well-folded protein of more 100 amino acids de novo remains a formidable challenge. Exploiting the promising biophysical features of the artificial protein Octarellin V, we improved this protein by directed evolution, thus creating a more stable and soluble protein: Octarellin V.1. Next, we obtained crystals of Octarellin V.1 in complex with crystallization chaperons and determined the tertiary structure. The experimental structure of Octarellin V.1 differs from its in silico design: the (αβα) sandwich architecture bears some resemblance to a Rossman-like fold instead of the intended TIM-barrel fold. This surprising result gave us a unique and attractive opportunity to test the state of the art in protein structure prediction, using this artificial protein free of any natural selection. We tested 13 automated webservers for protein structure prediction and found none of them to predict the actual structure. More than 50% of them predicted a TIM-barrel fold, i.e. the structure we set out to design more than 10years ago. In addition, local software runs that are human operated can sample a structure similar to the experimental one but fail in selecting it, suggesting that the scoring and ranking functions should be improved. We propose that artificial proteins could be used as tools to test the accuracy of protein structure prediction algorithms, because their lack of evolutionary pressure and unique sequences features.

    Organizational Affiliation: 

    GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium. Electronic address: c.vandeweerdt@ulg.ac.be.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AlphaRep-7 A294synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Octarellin V.1 B217synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.133α = 90
b = 42.021β = 106.35
c = 85.186γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Space AgencyBelgiumESA AO-2004-070

Revision History 

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references