Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.54 kDa 
• Atom Count: 2075 
• Modelled Residue Count: 251 
• Deposited Residue Count: 256 
• Unique protein chains: 1

3WW9

Crystal structure of the computationally designed Pizza6 protein

• PDB DOI: 10.2210/pdb3WW9/pdb

• Classification: DE NOVO PROTEIN
• Mutation(s): No 


• Deposited: 2014-06-17 Released: 2014-10-08 
• Deposition Author(s): Voet, A.R.D., Noguchi, H., Addy, C., Simoncini, D., Terada, D., Unzai, S., Park, S.Y., Zhang, K.Y.J., Tame, J.R.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.191 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 

Literature

Computational design of a self-assembling symmetrical beta-propeller protein.

Voet, A.R.D., Noguchi, H., Addy, C., Simoncini, D., Terada, D., Unzai, S., Park, S.Y., Zhang, K.Y.J., Tame, J.R.H.

(2014) Proc Natl Acad Sci U S A 111: 15102-15107

• PubMed: 25288768 
• DOI: 10.1073/pnas.1412768111
• Primary Citation of Related Structures:  
  3WW7, 3WW8, 3WW9, 3WWA, 3WWB, 3WWF


• PubMed Abstract: 
  

The modular structure of many protein families, such as β-propeller proteins, strongly implies that duplication played an important role in their evolution, leading to highly symmetrical intermediate forms. Previous attempts to create perfectly symmetrical propeller proteins have failed, however. We have therefore developed a new and rapid computational approach to design such proteins. As a test case, we have created a sixfold symmetrical β-propeller protein and experimentally validated the structure using X-ray crystallography. Each blade consists of 42 residues. Proteins carrying 2-10 identical blades were also expressed and purified. Two or three tandem blades assemble to recreate the highly stable sixfold symmetrical architecture, consistent with the duplication and fusion theory. The other proteins produce different monodisperse complexes, up to 42 blades (180 kDa) in size, which self-assemble according to simple symmetry rules. Our procedure is suitable for creating nano-building blocks from different protein templates of desired symmetry.

---

Organizational Affiliation: 

Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa 230-0045, Japan [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
pizza6 protein	A	256	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], G [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.191 
• R-Value Work: 0.158 
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.631	α = 90
b = 56.214	β = 90
c = 70.101	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-06-17 
• Released Date: 2014-10-08 
Deposition Author(s): Voet, A.R.D., Noguchi, H., Addy, C., Simoncini, D., Terada, D., Unzai, S., Park, S.Y., Zhang, K.Y.J., Tame, J.R.H.

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 1.1: 2014-11-05
  Changes: Database references