ELIC5 with cysteamine in 2:1:1 POPC:POPE:POPG nanodisc in open conformation

Experimental Data Snapshot

  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation.

Petroff, J.T.Dietzen, N.M.Santiago-McRae, E.Deng, B.Washington, M.S.Chen, L.J.Trent Moreland, K.Deng, Z.Rau, M.Fitzpatrick, J.A.J.Yuan, P.Joseph, T.T.Henin, J.Brannigan, G.Cheng, W.W.L.

(2022) Nat Commun 13: 7017

  • DOI: https://doi.org/10.1038/s41467-022-34813-5
  • Primary Citation of Related Structures:  
    8D63, 8D64, 8D65, 8D66, 8D67, 8VUW

  • PubMed Abstract: 

    Pentameric ligand-gated ion channels (pLGICs) mediate synaptic transmission and are sensitive to their lipid environment. The mechanism of phospholipid modulation of any pLGIC is not well understood. We demonstrate that the model pLGIC, ELIC (Erwinia ligand-gated ion channel), is positively modulated by the anionic phospholipid, phosphatidylglycerol, from the outer leaflet of the membrane. To explore the mechanism of phosphatidylglycerol modulation, we determine a structure of ELIC in an open-channel conformation. The structure shows a bound phospholipid in an outer leaflet site, and structural changes in the phospholipid binding site unique to the open-channel. In combination with streamlined alchemical free energy perturbation calculations and functional measurements in asymmetric liposomes, the data support a mechanism by which an anionic phospholipid stabilizes the activated, open-channel state of a pLGIC by specific, state-dependent binding to this site.

  • Organizational Affiliation

    Department of Anesthesiology, Washington University School of Medicine, Saint Louis, MO, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Erwinia chrysanthemi ligand-gated ion channel
A, B, C, D, E
322Dickeya chrysanthemiMutation(s): 5 
Membrane Entity: Yes 
Find proteins for P0C7B7 (Dickeya chrysanthemi)
Explore P0C7B7 
Go to UniProtKB:  P0C7B7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C7B7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGW (Subject of Investigation/LOI)
Query on PGW

Download Ideal Coordinates CCD File 
F [auth A],
H [auth A],
I [auth B],
K [auth C],
M [auth D]
(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
C40 H77 O10 P
DHL (Subject of Investigation/LOI)
Query on DHL

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
L [auth C],
N [auth D],
O [auth E]
C2 H7 N S
Experimental Data & Validation

Experimental Data

  • Resolution: 3.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM137957

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release