6YB1

Crystal structure of an antiparallel octameric transmembrane coiled coil K2-CCTM-VbIc

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

  • Deposited: 2020-03-15 Released: 2021-04-07 
  • Deposition Author(s): Kratochvil, H.T., Liu, L., Scott, A.J., Woolfson, D.N., DeGrado, W.F.
  • Funding Organization(s): Engineering and Physical Sciences Research Council, Biotechnology and Biological Sciences Research Council (BBSRC), European Research Council (ERC), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Constructing ion channels from water-soluble alpha-helical barrels.

Scott, A.J.Niitsu, A.Kratochvil, H.T.Lang, E.J.M.Sengel, J.T.Dawson, W.M.Mahendran, K.R.Mravic, M.Thomson, A.R.Brady, R.L.Liu, L.Mulholland, A.J.Bayley, H.DeGrado, W.F.Wallace, M.I.Woolfson, D.N.

(2021) Nat Chem 13: 643-650

  • DOI: https://doi.org/10.1038/s41557-021-00688-0
  • Primary Citation of Related Structures:  
    6YAZ, 6YB0, 6YB1, 6YB2

  • PubMed Abstract: 

    The design of peptides that assemble in membranes to form functional ion channels is challenging. Specifically, hydrophobic interactions must be designed between the peptides and at the peptide-lipid interfaces simultaneously. Here, we take a multi-step approach towards this problem. First, we use rational de novo design to generate water-soluble α-helical barrels with polar interiors, and confirm their structures using high-resolution X-ray crystallography. These α-helical barrels have water-filled lumens like those of transmembrane channels. Next, we modify the sequences to facilitate their insertion into lipid bilayers. Single-channel electrical recordings and fluorescent imaging of the peptides in membranes show monodisperse, cation-selective channels of unitary conductance. Surprisingly, however, an X-ray structure solved from the lipidic cubic phase for one peptide reveals an alternative state with tightly packed helices and a constricted channel. To reconcile these observations, we perform computational analyses to compare the properties of possible different states of the peptide.


  • Organizational Affiliation

    School of Chemistry, University of Bristol, Bristol, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
K2-CCTM-VbIc
A, B, C, D
33synthetic 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: 2.15 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.864α = 90
b = 47.864β = 90
c = 103.153γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited KingdomEP/G036764/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/J009784/1
European Research Council (ERC)United Kingdom340764
European Research Council (ERC)United Kingdom787173
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF32GM125217
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM122603
National Science Foundation (NSF, United States)United States1709506

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-05-26
    Changes: Database references
  • Version 1.2: 2021-07-14
    Changes: Database references