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 

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:  

  • 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 pro ...

    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.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium.,Department of Chemistry, Univeristy of Liège, Belgium.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.,Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.,GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium. Electronic address: maxifigueroa@udec.cl.,Laboratoire d'Enzymologie et Repliement des Protéines, Centre for Protein Engineering, University of Liège, Liège, Belgium.,Institute for Integrative Biology of the Cell (I2BC), UMT 9198, CEA, CNRS, Université Paris-Sud, Orsay, France.,Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States.,GIGA-Research, Molecular Biomimetics and Protein Engineering, University of Liège, Liège, Belgium. Electronic address: c.vandeweerdt@ulg.ac.be.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AlphaRep-7
A
294N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Octarellin V.1
B
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.233 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 73.133α = 90.00
b = 42.021β = 106.35
c = 85.186γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Database references