6G6P

Crystal structure of the computationally designed Ika8 protein: crystal packing No.2 in P63

Summary for 6G6P

• Entry DOI: 10.2210/pdb6g6p/pdb
• Descriptor: Ika8 (2 entities in total)
• Functional Keywords: artificial protein, de novo protein, wd40 proteins
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 34421.57

Authors

Noguchi, H.,Addy, C.,Simoncini, D.,Van Meervelt, L.,Schiex, T.,Zhang, K.Y.J.,Tame, J.R.H.,Voet, A.R.D. (deposition date: 2018-04-01, release date: 2018-11-28, Last modification date: 2024-05-08)

Primary citation

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.
Computational design of symmetrical eight-bladed beta-propeller proteins.
IUCrJ, 6:46-55, 2019

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.

PubMed: 30713702
DOI: 10.1107/S205225251801480X

Experimental method

X-RAY DIFFRACTION (2.4 Å)