7UDV

Designed pentameric proton channel LLQL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Transient water wires mediate selective proton transport in designed channel proteins.

Kratochvil, H.T.Watkins, L.C.Mravic, M.Thomaston, J.L.Nicoludis, J.M.Somberg, N.H.Liu, L.Hong, M.Voth, G.A.DeGrado, W.F.

(2023) Nat Chem 15: 1012-1021

  • DOI: https://doi.org/10.1038/s41557-023-01210-4
  • Primary Citation of Related Structures:  
    7UDV, 7UDW, 7UDX, 7UDY, 7UDZ

  • PubMed Abstract: 

    Selective proton transport through proteins is essential for forming and using proton gradients in cells. Protons are conducted along hydrogen-bonded 'wires' of water molecules and polar side chains, which, somewhat surprisingly, are often interrupted by dry apolar stretches in the conduction pathways, inferred from static protein structures. Here we hypothesize that protons are conducted through such dry spots by forming transient water wires, often highly correlated with the presence of the excess protons in the water wire. To test this hypothesis, we performed molecular dynamics simulations to design transmembrane channels with stable water pockets interspersed by apolar segments capable of forming flickering water wires. The minimalist designed channels conduct protons at rates similar to viral proton channels, and they are at least 10 6 -fold more selective for H + over Na + . These studies inform the mechanisms of biological proton conduction and the principles for engineering proton-conductive materials.


  • Organizational Affiliation

    Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA. huong.kratochvil@unc.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
De novo designed proton channel LLQL
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
26synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.247 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.53α = 90
b = 55.36β = 90
c = 82.71γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesK99GM138753
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM122603
National Science Foundation (NSF, United States)United StatesCHE1709506
Air Force Office of Scientific ResearchUnited StatesFA9550-19-1-0331

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references
  • Version 1.2: 2023-07-19
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description