9FDG | pdb_00009fdg

Solution structure of a de novo designed 12-stranded transmembrane beta-barrel in LDAO micelles.

• PDB DOI: https://doi.org/10.2210/pdb9FDG/pdb
• BMRB: 52384

• Classification: MEMBRANE PROTEIN
• Organism(s): synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-05-17 Released: 2024-10-16 
• Deposition Author(s): Muentener, T., Hiller, S.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Sculpting conducting nanopore size and shape through de novo protein design.

Berhanu, S., Majumder, S., Muentener, T., Whitehouse, J., Berner, C., Bera, A.K., Kang, A., Liang, B., Khan, N., Sankaran, B., Tamm, L.K., Brockwell, D.J., Hiller, S., Radford, S.E., Baker, D., Vorobieva, A.A.

(2024) Science 385: 282-288

• PubMed: 39024453 
• DOI: https://doi.org/10.1126/science.adn3796
• Primary Citation of Related Structures:  
  8UZL, 9FDG


• PubMed Abstract: 
  

  Transmembrane β-barrels have considerable potential for a broad range of sensing applications. Current engineering approaches for nanopore sensors are limited to naturally occurring channels, which provide suboptimal starting points. By contrast, de novo protein design can in principle create an unlimited number of new nanopores with any desired properties. Here we describe a general approach to designing transmembrane β-barrel pores with different diameters and pore geometries. Nuclear magnetic resonance and crystallographic characterization show that the designs are stably folded with structures resembling those of the design models. The designs have distinct conductances that correlate with their pore diameter, ranging from 110 picosiemens (~0.5 nanometer pore diameter) to 430 picosiemens (~1.1 nanometer pore diameter). Our approach opens the door to the custom design of transmembrane nanopores for sensing and sequencing applications.

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Organizational Affiliation: 
• Department of Biochemistry, The University of Washington, Seattle, WA, USA.
Institute for Protein Design, University of Washington, Seattle, WA, USA.
Biozentrum, University of Basel, Basel, Switzerland.
Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT.
Structural Biology Brussel, Vrije Universiteit Brussel, Brussels, Belgium.
VUB-VIB Center for Structural Biology, Brussels, Belgium.
Department of Molecular Physiology and Biological Physics and Center for Membrane and Cell Physiology, University of Virginia, Charlottesville, VA, USA.
Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
VIB Center for AI and Computational Biology, Belgium.

Biological Assembly 1  

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

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

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 20.35 kDa 
• Atom Count: 1,442 
• Modeled Residue Count: 179 
• Deposited Residue Count: 179 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TMB12sol9_3	A	179	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 500 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Muentener, T., Hiller, S.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release