Crystal structure of computationally designed protein XAX

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report

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Computational design of closely related proteins that adopt two well-defined but structurally divergent folds.

Wei, K.Y.Moschidi, D.Bick, M.J.Nerli, S.McShan, A.C.Carter, L.P.Huang, P.S.Fletcher, D.A.Sgourakis, N.G.Boyken, S.E.Baker, D.

(2020) Proc Natl Acad Sci U S A 117: 7208-7215

  • DOI: https://doi.org/10.1073/pnas.1914808117
  • Primary Citation of Related Structures:  
    6NX2, 6NXM, 6NY8, 6NYE, 6NYI, 6NYK, 6NZ1, 6NZ3, 6O0C, 6O0I

  • PubMed Abstract: 

    The plasticity of naturally occurring protein structures, which can change shape considerably in response to changes in environmental conditions, is critical to biological function. While computational methods have been used for de novo design of proteins that fold to a single state with a deep free-energy minimum [P.-S. Huang, S. E. Boyken, D. Baker, Nature 537, 320-327 (2016)], and to reengineer natural proteins to alter their dynamics [J. A. Davey, A. M. Damry, N. K. Goto, R. A. Chica, Nat. Chem. Biol. 13, 1280-1285 (2017)] or fold [P. A. Alexander, Y. He, Y. Chen, J. Orban, P. N. Bryan, Proc. Natl. Acad. Sci. U.S.A. 106, 21149-21154 (2009)], the de novo design of closely related sequences which adopt well-defined but structurally divergent structures remains an outstanding challenge. We designed closely related sequences (over 94% identity) that can adopt two very different homotrimeric helical bundle conformations-one short (∼66 Å height) and the other long (∼100 Å height)-reminiscent of the conformational transition of viral fusion proteins. Crystallographic and NMR spectroscopic characterization shows that both the short- and long-state sequences fold as designed. We sought to design bistable sequences for which both states are accessible, and obtained a single designed protein sequence that populates either the short state or the long state depending on the measurement conditions. The design of sequences which are poised to adopt two very different conformations sets the stage for creating large-scale conformational switches between structurally divergent forms.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Design construct XAX
A, B, C
98synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.179α = 90
b = 75.322β = 90
c = 96.944γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30 GM124169
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM124149

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-22
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Data collection, Database references