Crystal structure of the computationally designed Ika8 protein: crystal packing No.1 in P63

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report

This is version 1.1 of the entry. See complete history


Computational design of symmetrical eight-bladed beta-propeller proteins.

Noguchi, H.Addy, C.Simoncini, D.Wouters, S.Mylemans, B.Van Meervelt, L.Schiex, T.Zhang, K.Y.J.Tame, J.R.H.Voet, A.R.D.

(2019) IUCrJ 6: 46-55

  • DOI: https://doi.org/10.1107/S205225251801480X
  • Primary Citation of Related Structures:  
    6G6M, 6G6N, 6G6O, 6G6P, 6G6Q

  • PubMed Abstract: 

    β-Propeller proteins form one of the largest families of protein structures, with a pseudo-symmetrical fold made up of subdomains called blades. They are not only abundant but are also involved in a wide variety of cellular processes, often by acting as a platform for the assembly of protein complexes. WD40 proteins are a subfamily of propeller proteins with no intrinsic enzymatic activity, but their stable, modular architecture and versatile surface have allowed evolution to adapt them to many vital roles. By computationally reverse-engineering the duplication, fusion and diversification events in the evolutionary history of a WD40 protein, a perfectly symmetrical homologue called Tako8 was made. If two or four blades of Tako8 are expressed as single polypeptides, they do not self-assemble to complete the eight-bladed architecture, which may be owing to the closely spaced negative charges inside the ring. A different computational approach was employed to redesign Tako8 to create Ika8, a fourfold-symmetrical protein in which neighbouring blades carry compensating charges. Ika2 and Ika4, carrying two or four blades per subunit, respectively, were found to assemble spontaneously into a complete eight-bladed ring in solution. These artificial eight-bladed rings may find applications in bionanotechnology and as models to study the folding and evolution of WD40 proteins.

  • Organizational Affiliation

    Laboratory of Biomolecular Modelling and Design, Department of Chemistry, KU Leuven, Celestijnenlaan 200G, 3001 Leuven, Belgium.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
324synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.238 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 218.609α = 90
b = 218.609β = 90
c = 53.569γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
BelgiumG0E4717N, G0F9316N, G051917N
Japan Science and TechnologyJapan16H04779

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references