5CWF

Crystal structure of de novo designed helical repeat protein DHR8

• PDB DOI:  https://doi.org/10.2210/pdb5CWF/pdb

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


• Deposited: 2015-07-28 Released: 2015-12-16 
• Deposition Author(s): Bhabha, G., Ekiert, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.220 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 

Literature

Exploring the repeat protein universe through computational protein design.

Brunette, T.J., Parmeggiani, F., Huang, P.S., Bhabha, G., Ekiert, D.C., Tsutakawa, S.E., Hura, G.L., Tainer, J.A., Baker, D.

(2015) Nature 528: 580-584

• PubMed: 26675729 
• DOI: https://doi.org/10.1038/nature16162
• Primary Citation of Related Structures:  
  5CWB, 5CWC, 5CWD, 5CWF, 5CWG, 5CWH, 5CWI, 5CWJ, 5CWK, 5CWL, 5CWM, 5CWN, 5CWO, 5CWP, 5CWQ


• PubMed Abstract: 
  

A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed of multiple tandem copies of a modular structure unit are widespread in nature and have critical roles in molecular recognition, signalling, and other essential biological processes. Naturally occurring repeat proteins have been re-engineered for molecular recognition and modular scaffolding applications. Here we use computational protein design to investigate the space of folded structures that can be generated by tandem repeating a simple helix-loop-helix-loop structural motif. Eighty-three designs with sequences unrelated to known repeat proteins were experimentally characterized. Of these, 53 are monomeric and stable at 95 °C, and 43 have solution X-ray scattering spectra consistent with the design models. Crystal structures of 15 designs spanning a broad range of curvatures are in close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5 Å. Our results show that existing repeat proteins occupy only a small fraction of the possible repeat protein sequence and structure space and that it is possible to design novel repeat proteins with precisely specified geometries, opening up a wide array of new possibilities for biomolecular engineering.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 86.78 kDa 
• Atom Count: 5,923 
• Modelled Residue Count: 704 
• Deposited Residue Count: 764 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed helical repeat protein	A, B, C, D	191	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	AA [auth C], BA [auth C], CA [auth C], DA [auth C], E [auth A], EA [auth C], F [auth A], FA [auth D], G [auth A], GA [auth D], H [auth A], HA [auth D], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], L [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth C], Y [auth C], Z [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.220 
• R-Value Work: 0.194 
• R-Value Observed: 0.195 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.69	α = 90
b = 76.36	β = 90
c = 133.14	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-16 
Deposition Author(s): Bhabha, G., Ekiert, D.C.

Revision History  

• Version 1.0: 2015-12-16
  Type: Initial release
  
• Version 1.1: 2015-12-30
  Changes: Database references
• Version 1.2: 2016-01-06
  Changes: Database references