6X9Z | pdb_00006x9z

De novo design of transmembrane beta-barrels

• PDB DOI: https://doi.org/10.2210/pdb6X9Z/pdb

• Classification: DE NOVO PROTEIN
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2020-06-03 Released: 2021-02-17 
• Deposition Author(s): Bera, A.K., Vorobieva, A.A., Kang, A.S., Baker, D.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.274 (Depositor), 0.271 (DCC) 
• R-Value Work: 
  0.260 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.261 (Depositor) 

Starting Model: in silico

Literature

De novo design of transmembrane beta barrels.

Vorobieva, A.A., White, P., Liang, B., Horne, J.E., Bera, A.K., Chow, C.M., Gerben, S., Marx, S., Kang, A., Stiving, A.Q., Harvey, S.R., Marx, D.C., Khan, G.N., Fleming, K.G., Wysocki, V.H., Brockwell, D.J., Tamm, L.K., Radford, S.E., Baker, D.

(2021) Science 371

• PubMed: 33602829 
• DOI: https://doi.org/10.1126/science.abc8182
• Primary Citation Related Structures: 
  6X1K, 6X9Z


• PubMed Abstract: 
  

  Transmembrane β-barrel proteins (TMBs) are of great interest for single-molecule analytical technologies because they can spontaneously fold and insert into membranes and form stable pores, but the range of pore properties that can be achieved by repurposing natural TMBs is limited. We leverage the power of de novo computational design coupled with a "hypothesis, design, and test" approach to determine TMB design principles, notably, the importance of negative design to slow β-sheet assembly. We design new eight-stranded TMBs, with no homology to known TMBs, that insert and fold reversibly into synthetic lipid membranes and have nuclear magnetic resonance and x-ray crystal structures very similar to the computational models. These advances should enable the custom design of pores for a wide range of applications.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, USA.
Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA 22903, USA.
Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Department of Molecular Engineering and Sciences, University of Washington, Seattle, WA 98195, USA.
Department of Chemistry and Biochemistry, Resource for Native Mass Spectrometry Guided Structural Biology, The Ohio State University, Columbus, OH 43210, USA.
TC Jenkins Department of Biophysics Johns Hopkins University, Baltimore, MD 21218, USA.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 13.42 kDa 
• Atom Count: 947 
• Modeled Residue Count: 120 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transmembrane beta-barrels	A	124	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.274 (Depositor), 0.271 (DCC) 
• R-Value Work:  0.260 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.261 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.083	α = 90
b = 51.083	β = 90
c = 116.71	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-02-17 
Deposition Author(s): Bera, A.K., Vorobieva, A.A., Kang, A.S., Baker, D.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2021-02-17
  Type: Initial release
  
• Version 1.1: 2021-03-03
  Changes: Database references
• Version 1.2: 2024-03-06
  Changes: Data collection, Database references
• Version 1.3: 2024-04-03
  Changes: Refinement description