8UZL | pdb_00008uzl

Designed Transmembrane beta-barrel- TMB10_163


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.262 (Depositor), 0.264 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: other
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wwPDB Validation 3D Report Full Report

Validation slider image for 8UZL

This is version 1.1 of the entry. See complete history

Literature

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

Berhanu, S.Majumder, S.Muntener, 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

  • DOI: https://doi.org/10.1126/science.adn3796
  • Primary Citation 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.


  • Organizational Affiliation
    • Department of Biochemistry, The University of Washington, Seattle, WA, USA.

Macromolecule Content 

  • Total Structure Weight: 65.99 kDa 
  • Atom Count: 4,535 
  • Modeled Residue Count: 568 
  • Deposited Residue Count: 596 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Designed Transmembrane beta-barrel TMB10_163
A, B, C, D
149synthetic constructMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.262 (Depositor), 0.264 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.628α = 90
b = 52.552β = 93.675
c = 100.05γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-07-31
    Changes: Database references