Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 36.95 kDa 
• Atom Count: 2512 
• Residue Count: 319 
• Unique protein chains: 1

4HB5

Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR267.

• DOI: 10.2210/pdb4HB5/pdb

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


• Deposited: 2012-09-27 Released: 2012-10-10 
• Deposition Author(s): Vorobiev, S., Su, M., Parmeggiani, F., Seetharaman, J., Huang, P.-S., Maglaqui, M., Xiao, R., Lee, D., Everett, J.K., Acton, T.B., Baker, D., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.236 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Computational design of self-assembling cyclic protein homo-oligomers.

Fallas, J.A., Ueda, G., Sheffler, W., Nguyen, V., McNamara, D.E., Sankaran, B., Pereira, J.H., Parmeggiani, F., Brunette, T.J., Cascio, D., Yeates, T.R., Zwart, P., Baker, D.

(2017) Nat Chem 9: 353-360

• PubMed: 28338692 
• DOI: 10.1038/nchem.2673
• Primary Citation of Related Structures:  
  4HB5, 4GPM, 4HXT, 5HRZ, 5HRY, 5HS0, 5K7V, 5KBA, 5KWD, 4GMR


• PubMed Abstract: 
  

Self-assembling cyclic protein homo-oligomers play important roles in biology, and the ability to generate custom homo-oligomeric structures could enable new approaches to probe biological function. Here we report a general approach to design cyclic homo-oligomers that employs a new residue-pair-transform method to assess the designability of a protein-protein interface. This method is sufficiently rapid to enable the systematic enumeration of cyclically docked arrangements of a monomer followed by sequence design of the newly formed interfaces. We use this method to design interfaces onto idealized repeat proteins that direct their assembly into complexes that possess cyclic symmetry. Of 96 designs that were characterized experimentally, 21 were found to form stable monodisperse homo-oligomers in solution, and 15 (four homodimers, six homotrimers, six homotetramers and one homopentamer) had solution small-angle X-ray scattering data consistent with the design models. X-ray crystal structures were obtained for five of the designs and each is very close to their corresponding computational model.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered Protein	A, B	169	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 0.236 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.977	α = 90
b = 45.469	β = 107.17
c = 63.152	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-09-27 
• Released Date: 2012-10-10 
Deposition Author(s): Vorobiev, S., Su, M., Parmeggiani, F., Seetharaman, J., Huang, P.-S., Maglaqui, M., Xiao, R., Lee, D., Everett, J.K., Acton, T.B., Baker, D., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History 

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2017-04-12
  Changes: Database references