Computational Design of Self-Assembling Cyclic Protein Homooligomers

Experimental Data Snapshot

  • Resolution: 3.17 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.213 

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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

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

  • 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.

  • Organizational Affiliation

    Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Designed protein HR00C3
A, B, C
288synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.17 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.213 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.005α = 90
b = 159.005β = 90
c = 94.982γ = 120
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Author supporting evidence
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references