6G6M

Crystal structure of the computationally designed Tako8 protein in P42212


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1107/S205225251801480X
  • Structures With Same Primary Citation

  • 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 ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tako8
A
325synthetic constructMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.401α = 90
b = 90.401β = 90
c = 91.854γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


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

Revision History 

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