4UOS

Thermodynamic hyperstability in parametrically designed helical bundles

• PDB DOI:  https://doi.org/10.2210/pdb4UOS/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-06-09 Released: 2014-11-05 
• Deposition Author(s): Oberdorfer, G., Huang, P., Pei, X.Y., Xu, C., Gonen, T., Nannenga, B., DiMaio, D., Rogers, J., Luisi, B.F., Baker, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.206 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 

Literature

High Thermodynamic Stability of Parametrically Designed Helical Bundles

Huang, P., Oberdorfer, G., Xu, C., Pei, X.Y., Nannenga, B.L., Rogers, J.M., Dimaio, F., Gonen, T., Luisi, B., Baker, D.

(2014) Science 346: 481

• PubMed: 25342806 
• DOI: https://doi.org/10.1126/science.1257481
• Primary Citation of Related Structures:  
  4TQL, 4UOS, 4UOT


• PubMed Abstract: 
  

We describe a procedure for designing proteins with backbones produced by varying the parameters in the Crick coiled coil-generating equations. Combinatorial design calculations identify low-energy sequences for alternative helix supercoil arrangements, and the helices in the lowest-energy arrangements are connected by loop building. We design an antiparallel monomeric untwisted three-helix bundle with 80-residue helices, an antiparallel monomeric right-handed four-helix bundle, and a pentameric parallel left-handed five-helix bundle. The designed proteins are extremely stable (extrapolated ΔGfold > 60 kilocalories per mole), and their crystal structures are close to those of the design models with nearly identical core packing between the helices. The approach enables the custom design of hyperstable proteins with fine-tuned geometries for a wide range of applications.

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Organizational Affiliation: 

Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 22.44 kDa 
• Atom Count: 1,857 
• Modelled Residue Count: 188 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DESIGNED HELICAL BUNDLE	A	191	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.206 
• R-Value Work: 0.193 
• R-Value Observed: 0.194 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.46	α = 90
b = 72.15	β = 92.9
c = 51.26	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
ACORN	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-05 
Deposition Author(s): Oberdorfer, G., Huang, P., Pei, X.Y., Xu, C., Gonen, T., Nannenga, B., DiMaio, D., Rogers, J., Luisi, B.F., Baker, D.

Revision History  

• Version 1.0: 2014-11-05
  Type: Initial release
  
• Version 1.1: 2014-11-19
  Changes: Database references
• Version 1.2: 2016-12-14
  Changes: Data collection