9EX6 | pdb_00009ex6

CryoEM structure of sTeLIC nanodisc in closed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9EX6

This is version 1.2 of the entry. See complete history

Literature

Vestibular modulation by stimulant derivatives in a pentameric ligand-gated ion channel.

Karlsson, E.Anden, O.Fan, C.Fourati, Z.Haouz, A.Zhuang, Y.Howard, R.J.Delarue, M.Lindahl, E.

(2025) Br J Pharmacol 182: 2790-2802

  • DOI: https://doi.org/10.1111/bph.70011
  • Primary Citation Related Structures: 
    9EWA, 9EWL, 9EX4, 9EX6, 9F5N, 9F5O

  • PubMed Abstract: 

    Allosteric modulation of pentameric ligand-gated ion channels (pLGICs) are critical for the action of neurotransmitters and many psychoactive drugs. However, details of their modulatory mechanisms remain unclear, especially beyond the orthosteric neurotransmitter-binding sites. The recently reported prokaryotic symbiont of Tevnia jerichonana ligand-gated ion channel (sTeLIC), a pH-gated homologue of eukaryotic receptors in the pLGIC family, is thought to be modulated by aromatic compounds via a relatively uncharacterised modulatory site in the extracellular vestibule. We have characterised the effects of psychostimulant derivatives on sTeLIC using two-electrode voltage-clamp electrophysiology in the presence and absence of engineered mutations, and determined X-ray and cryo-EM structures of the channel in both closed and open states. We have shown that sTeLIC is sensitive to potentiation by several amphiphilic compounds, which preferentially bind to a vestibular pocket in the contracted open-state extracellular domain. This work provides a detailed structure-function mechanism for allosteric potentiation via a noncanonical ligand site, with potential conservation of the eukaryotic pentameric ligand-gated ion channels.


  • Organizational Affiliation
    • Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Solna, Sweden.

Macromolecule Content 

  • Total Structure Weight: 191.53 kDa 
  • Atom Count: 13,115 
  • Modeled Residue Count: 1,550 
  • Deposited Residue Count: 1,600 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cys-loop ligand-gated ion channel
A, B, C, D, E
320endosymbiont of Tevnia jerichonana (vent Tica)Mutation(s): 0 
Gene Names: TevJSym_bc00020
Membrane Entity: Yes 
UniProt
Find proteins for G2FID1 (endosymbiont of Tevnia jerichonana)
Explore G2FID1 
Go to UniProtKB:  G2FID1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2FID1
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C14
(Subject of Investigation/LOI)

Query on C14



Download:Ideal Coordinates CCD File
EA [auth D],
I [auth A],
LA [auth E],
Q [auth B],
X [auth C]
TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
D12
(Subject of Investigation/LOI)

Query on D12



Download:Ideal Coordinates CCD File
BA [auth D]
CA [auth D]
F [auth A]
G [auth A]
IA [auth E]
BA [auth D],
CA [auth D],
F [auth A],
G [auth A],
IA [auth E],
JA [auth E],
N [auth B],
O [auth B],
U [auth C],
V [auth C]
DODECANE
C12 H26
SNRUBQQJIBEYMU-UHFFFAOYSA-N
D10
(Subject of Investigation/LOI)

Query on D10



Download:Ideal Coordinates CCD File
GA [auth D],
K [auth A],
NA [auth E],
S [auth B],
Z [auth C]
DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
OCT
(Subject of Investigation/LOI)

Query on OCT



Download:Ideal Coordinates CCD File
AA [auth D]
DA [auth D]
H [auth A]
HA [auth E]
KA [auth E]
AA [auth D],
DA [auth D],
H [auth A],
HA [auth E],
KA [auth E],
L [auth A],
M [auth B],
P [auth B],
T [auth C],
W [auth C]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
HEX
(Subject of Investigation/LOI)

Query on HEX



Download:Ideal Coordinates CCD File
FA [auth D],
J [auth A],
MA [auth E],
R [auth B],
Y [auth C]
HEXANE
C6 H14
VLKZOEOYAKHREP-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research Council--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-26
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Data collection, Database references
  • Version 1.2: 2025-07-09
    Changes: Data collection