6HJX

X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) 7'C pore mutant (L238C) in complex with nanobody 72


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 

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Ligand Structure Quality Assessment 


This is version 1.2 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: 10.1038/s41589-019-0369-4
  • Primary Citation of Related Structures:  
    6HK0, 6HJY, 6HJX

  • 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 ...

    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

    Laboratory of Structural Neurobiology, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium. chris.ulens@kuleuven.be.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cys-loop ligand-gated ion channelA306Dickeya chrysanthemiMutation(s): 3 
Membrane Entity: Yes 
UniProt
Find proteins for P0C7B7 (Dickeya chrysanthemi)
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Go to UniProtKB:  P0C7B7
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cys-loop ligand-gated ion channelB309Dickeya chrysanthemiMutation(s): 3 
Membrane Entity: Yes 
UniProt
Find proteins for P0C7B7 (Dickeya chrysanthemi)
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Go to UniProtKB:  P0C7B7
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cys-loop ligand-gated ion channelC312Dickeya chrysanthemiMutation(s): 3 
Membrane Entity: Yes 
UniProt
Find proteins for P0C7B7 (Dickeya chrysanthemi)
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Go to UniProtKB:  P0C7B7
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Cys-loop ligand-gated ion channelD310Dickeya chrysanthemiMutation(s): 3 
Membrane Entity: Yes 
UniProt
Find proteins for P0C7B7 (Dickeya chrysanthemi)
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Go to UniProtKB:  P0C7B7
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Cys-loop ligand-gated ion channelE307Dickeya chrysanthemiMutation(s): 3 
Membrane Entity: Yes 
UniProt
Find proteins for P0C7B7 (Dickeya chrysanthemi)
Explore P0C7B7 
Go to UniProtKB:  P0C7B7
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
nanobody 72F, G, H, I, J124Lama glamaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PTY (Subject of Investigation/LOI)
Query on PTY

Download Ideal Coordinates CCD File 
L [auth A]PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
 Ligand Interaction
LMT (Subject of Investigation/LOI)
Query on LMT

Download Ideal Coordinates CCD File 
M [auth A], N [auth B], P [auth C], S [auth D], U [auth E]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
P6G
Query on P6G

Download Ideal Coordinates CCD File 
K [auth A], O [auth B], T [auth D], V [auth E]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
MES
Query on MES

Download Ideal Coordinates CCD File 
Q [auth C]2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
R [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.206 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.251α = 90
b = 156.277β = 102.88
c = 102.496γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



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