9NGS | pdb_00009ngs

ELIC with propylamine facing ECD inwards in liposomes with 2:1:1 POPC:POPE:POPG

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Dickeya dadantii
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2025-02-22 Released: 2025-07-23 
  • Deposition Author(s): Dalal, V., Cheng, W.W.L.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), American Heart Association

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures of a pentameric ligand-gated ion channel in liposomes.

Dalal, V.Tan, B.K.Xu, H.Cheng, W.W.L.

(2025) Elife 14

  • DOI: https://doi.org/10.7554/eLife.106728
  • Primary Citation of Related Structures:  
    9NGF, 9NGG, 9NGI, 9NGQ, 9NGR, 9NGS, 9NH4

  • PubMed Abstract: 

    Detergents and lipid nanodiscs affect the cryo-EM structures of pentameric ligand-gated ion channels (pLGICs) including ELIC. To determine the structure of a pLGIC in a membrane environment that supports ion channel function, we performed single particle cryo-EM of ELIC in liposomes. ELIC activation and desensitization were confirmed in liposomes with a stopped-flow thallium flux assay. Using WT ELIC and a non-desensitizing mutant (ELIC5), we captured resting, activated, and desensitized structures at high resolution. In the desensitized structure, the ion conduction pore has a constriction at the 9' leucine of the pore-lining M2 helix, indicating that 9' is the desensitization gate in ELIC. The agonist-bound structures of ELIC in liposomes are distinct from those in nanodiscs. In general, the transmembrane domain is more loosely packed in liposomes compared to nanodiscs. It has been suggested that large nanodiscs are superior for supporting membrane protein function. However, ELIC localizes to the rim of large circularized nanodiscs, and structures of ELIC in large nanodiscs deviate from the liposome structures more than those in small nanodiscs. Using liposomes for cryo-EM structure determination of a pLGIC increases our confidence that the structures are snapshots of functional states.


  • Organizational Affiliation

    Department of Anesthesiology, Washington University School of Medicine, St Louis, United States.


Macromolecules
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 dadantiiMutation(s): 0 
Gene Names: Dda3937_00520
UniProt
Find proteins for E0SJQ4 (Dickeya dadantii (strain 3937))
Explore E0SJQ4 
Go to UniProtKB:  E0SJQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0SJQ4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3CN (Subject of Investigation/LOI)
Query on 3CN

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
L [auth C],
M [auth D],
N [auth E]
3-AMINOPROPANE
C3 H9 N
WGYKZJWCGVVSQN-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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
American Heart AssociationUnited States24POST1189869

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-23
    Type: Initial release
  • Version 1.1: 2025-07-30
    Changes: Data collection, Database references