6HJY

X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) Delta8 truncation mutant in complex with nanobody 72


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

A lipid site shapes the agonist response of a pentameric ligand-gated ion channel.

Henault, C.M.Govaerts, C.Spurny, R.Brams, M.Estrada-Mondragon, A.Lynch, J.Bertrand, D.Pardon, E.Evans, G.L.Woods, K.Elberson, B.W.Cuello, L.G.Brannigan, G.Nury, H.Steyaert, J.Baenziger, J.E.Ulens, C.

(2019) Nat Chem Biol 15: 1156-1164

  • DOI: https://doi.org/10.1038/s41589-019-0369-4
  • Primary Citation of Related Structures:  
    6HJX, 6HJY, 6HK0

  • PubMed Abstract: 

    Phospholipids are key components of cellular membranes and are emerging as important functional regulators of different membrane proteins, including pentameric ligand-gated ion channels (pLGICs). Here, we take advantage of the prokaryote channel ELIC (Erwinia ligand-gated ion channel) as a model to understand the determinants of phospholipid interactions in this family of receptors. A high-resolution structure of ELIC in a lipid-bound state reveals a phospholipid site at the lower half of pore-forming transmembrane helices M1 and M4 and at a nearby site for neurosteroids, cholesterol or general anesthetics. This site is shaped by an M4-helix kink and a Trp-Arg-Pro triad that is highly conserved in eukaryote GABA A/C and glycine receptors. A combined approach reveals that M4 is intrinsically flexible and that M4 deletions or disruptions of the lipid-binding site accelerate desensitization in ELIC, suggesting that lipid interactions shape the agonist response. Our data offer a structural context for understanding lipid modulation in pLGICs.


  • Organizational Affiliation

    Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cys-loop ligand-gated ion channel277Dickeya chrysanthemiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C7B7 (Dickeya chrysanthemi)
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Go to UniProtKB:  P0C7B7
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UniProt GroupP0C7B7
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cys-loop ligand-gated ion channel
B, C
280Dickeya chrysanthemiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C7B7 (Dickeya chrysanthemi)
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Go to UniProtKB:  P0C7B7
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UniProt GroupP0C7B7
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Cys-loop ligand-gated ion channel276Dickeya chrysanthemiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C7B7 (Dickeya chrysanthemi)
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Go to UniProtKB:  P0C7B7
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UniProt GroupP0C7B7
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Cys-loop ligand-gated ion channel278Dickeya chrysanthemiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C7B7 (Dickeya chrysanthemi)
Explore P0C7B7 
Go to UniProtKB:  P0C7B7
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UniProt GroupP0C7B7
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
nanobody 72
F, J
124Lama glamaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
nanobody 72
G, H, I
123Lama glamaMutation(s): 0 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.675α = 90
b = 155.093β = 103.08
c = 101.618γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-09
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary