6D0T

De novo design of a fluorescence-activating beta barrel - BB1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

De novo design of a fluorescence-activating beta-barrel.

Dou, J.Vorobieva, A.A.Sheffler, W.Doyle, L.A.Park, H.Bick, M.J.Mao, B.Foight, G.W.Lee, M.Y.Gagnon, L.A.Carter, L.Sankaran, B.Ovchinnikov, S.Marcos, E.Huang, P.S.Vaughan, J.C.Stoddard, B.L.Baker, D.

(2018) Nature 561: 485-491

  • DOI: 10.1038/s41586-018-0509-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The regular arrangements of β-strands around a central axis in β-barrels and of α-helices in coiled coils contrast with the irregular tertiary structures of most globular proteins, and have fascinated structural biologists since they were first disco ...

    The regular arrangements of β-strands around a central axis in β-barrels and of α-helices in coiled coils contrast with the irregular tertiary structures of most globular proteins, and have fascinated structural biologists since they were first discovered. Simple parametric models have been used to design a wide range of α-helical coiled-coil structures, but to date there has been no success with β-barrels. Here we show that accurate de novo design of β-barrels requires considerable symmetry-breaking to achieve continuous hydrogen-bond connectivity and eliminate backbone strain. We then build ensembles of β-barrel backbone models with cavity shapes that match the fluorogenic compound DFHBI, and use a hierarchical grid-based search method to simultaneously optimize the rigid-body placement of DFHBI in these cavities and the identities of the surrounding amino acids to achieve high shape and chemical complementarity. The designs have high structural accuracy and bind and fluorescently activate DFHBI in vitro and in Escherichia coli, yeast and mammalian cells. This de novo design of small-molecule binding activity, using backbones custom-built to bind the ligand, should enable the design of increasingly sophisticated ligand-binding proteins, sensors and catalysts that are not limited by the backbone geometries available in known protein structures.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BB1
A, B
120N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.760α = 90.00
b = 32.270β = 100.64
c = 81.650γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
xia2data scaling
PHENIXrefinement
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (United States)United StatesDE-AC02-05CH11231
National Science Foundation (United States)United StatesCHE1332907
Howard Hughes Medical InstituteUnited States--

Revision History 

  • Version 1.0: 2018-09-19
    Type: Initial release
  • Version 1.1: 2018-09-26
    Type: Data collection, Database references
  • Version 1.2: 2018-10-17
    Type: Data collection, Database references