6TJ1

Crystal structure of a de novo designed hexameric helical-bundle protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Computational design of transmembrane pores.

Xu, C.Lu, P.Gamal El-Din, T.M.Pei, X.Y.Johnson, M.C.Uyeda, A.Bick, M.J.Xu, Q.Jiang, D.Bai, H.Reggiano, G.Hsia, Y.Brunette, T.J.Dou, J.Ma, D.Lynch, E.M.Boyken, S.E.Huang, P.S.Stewart, L.DiMaio, F.Kollman, J.M.Luisi, B.F.Matsuura, T.Catterall, W.A.Baker, D.

(2020) Nature 585: 129-134

  • DOI: https://doi.org/10.1038/s41586-020-2646-5
  • Primary Citation of Related Structures:  
    6M6Z, 6O35, 6TJ1, 6TMS

  • PubMed Abstract: 

    Transmembrane channels and pores have key roles in fundamental biological processes 1 and in biotechnological applications such as DNA nanopore sequencing 2-4 , resulting in considerable interest in the design of pore-containing proteins. Synthetic amphiphilic peptides have been found to form ion channels 5,6 , and there have been recent advances in de novo membrane protein design 7,8 and in redesigning naturally occurring channel-containing proteins 9,10 . However, the de novo design of stable, well-defined transmembrane protein pores that are capable of conducting ions selectively or are large enough to enable the passage of small-molecule fluorophores remains an outstanding challenge 11,12 . Here we report the computational design of protein pores formed by two concentric rings of α-helices that are stable and monodisperse in both their water-soluble and their transmembrane forms. Crystal structures of the water-soluble forms of a 12-helical pore and a 16-helical pore closely match the computational design models. Patch-clamp electrophysiology experiments show that, when expressed in insect cells, the transmembrane form of the 12-helix pore enables the passage of ions across the membrane with high selectivity for potassium over sodium; ion passage is blocked by specific chemical modification at the pore entrance. When incorporated into liposomes using in vitro protein synthesis, the transmembrane form of the 16-helix pore-but not the 12-helix pore-enables the passage of biotinylated Alexa Fluor 488. A cryo-electron microscopy structure of the 16-helix transmembrane pore closely matches the design model. The ability to produce structurally and functionally well-defined transmembrane pores opens the door to the creation of designer channels and pores for a wide variety of applications.


  • Organizational Affiliation

    Institute for Protein Design, University of Washington, Seattle, WA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
De novo designed WSHC6
A, B, C
93synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
purification tag6synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.72α = 90
b = 54.13β = 90
c = 79.17γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
AutoSolphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United States Department of Agriculture (USDA)United StatesFA9550-18-1-0297

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-29
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references