PDB-9ewl: The sTeLIC pentameric Ligand-Gated Ion Channel (wild-type) in com...

ID or keywords:

Entry

Database: PDB / ID: 9ewl

Title

The sTeLIC pentameric Ligand-Gated Ion Channel (wild-type) in complex with 4-bromoamphetamine

Components

Cys-loop ligand-gated ion channel

Keywords

MEMBRANE PROTEIN / Ion channel

Function / homology

Function and homology information

extracellular ligand-gated monoatomic ion channel activity / transmembrane signaling receptor activity / metal ion binding / membrane
Similarity search - Function

Biological species

endosymbiont of Tevnia jerichonana (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.2 Å

Authors

Fourati, Z. / Delarue, M.

Funding support

France, 1items

Citation

Journal: Br J Pharmacol / Year: 2025
Title: Vestibular modulation by stimulant derivatives in a pentameric ligand-gated ion channel.
Authors: Emelia Karlsson / Olivia Andén / Chen Fan / Zaineb Fourati / Ahmed Haouz / Yuxuan Zhuang / Rebecca J Howard / Marc Delarue / Erik Lindahl /

Abstract: BACKGROUND AND PURPOSE: Allosteric modulation of pentameric ligand-gated ion channels (pLGICs) are critical for the action of neurotransmitters and many psychoactive drugs. However, details of their ...
EXPERIMENTAL APPROACH: We have characterised the effects of psychostimulant derivatives on sTeLIC using two-electrode voltage-clamp electrophysiology in the presence and absence of engineered ...
KEY RESULTS: 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.
CONCLUSIONS AND IMPLICATIONS: This work provides a detailed structure-function mechanism for allosteric potentiation via a noncanonical ligand site, with potential conservation of the eukaryotic ...

History

Deposition	Apr 4, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 26, 2025	Provider: repository / Type: Initial release
Revision 1.1	May 28, 2025	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9ewl.cif.gz	340.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9ewl.ent.gz		Display	PDB format
PDBx/mmJSON format	9ewl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ew/9ewl ftp://data.pdbj.org/pub/pdb/validation_reports/ew/9ewl	HTTPS FTP

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Related structure data

Related structure data	50030C 50031C 50194C 50195C 9ewaC 9ex4C 9ex6C 9f5nC 9f5oC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (5) #71 - Nov 2005 Acetylcholine Receptor similarity (5)

Deposited unit

AAA: Cys-loop ligand-gated ion channel

BBB: Cys-loop ligand-gated ion channel

CCC: Cys-loop ligand-gated ion channel

DDD: Cys-loop ligand-gated ion channel

EEE: Cys-loop ligand-gated ion channel

hetero molecules

189 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	218.380, 114.320, 142.440
Angle α, β, γ (deg.)	90.000, 113.052, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	Chains AAA BBB
2	2	Chains AAA CCC
3	3	Chains AAA DDD
4	4	Chains AAA EEE
5	5	Chains BBB CCC
6	6	Chains BBB DDD
7	7	Chains BBB EEE
8	8	Chains CCC DDD
9	9	Chains CCC EEE
10	10	Chains DDD EEE

NCS domain segments:

Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 7 - 316 / Label seq-ID: 7 - 316

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10

#1: Protein

Cys-loop ligand-gated ion channel

Mass: 37310.820 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

endosymbiont of Tevnia jerichonana (vent Tica) (bacteria)
Gene: TevJSym_bc00020 / Production host:

Escherichia (bacteria) / References: UniProt: G2FID1

#2: Sugar

ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside

Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₃₀O₆ / Comment: detergent*YM

#3: Chemical

ChemComp-A1H7R / (2S)-1-(4-bromophenyl)propan-2-amine / N,N'-(9-{[4-(dimethylamino)phenyl]amino}acridine-3,6-diyl)bis(3-pyrrolidin-1-ylpropanamide)

Mass: 214.102 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₉H₁₂BrN / Feature type: SUBJECT OF INVESTIGATION

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

Y

Has protein modification

N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 4.38 Å³/Da / Density % sol: 71.95 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 100 mM Tris pH 8.0; 150 mM MgCl2; 3% DMSO; 32% PEG 200

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.919 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 18, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.919 Å / Relative weight: 1
Reflection	Resolution: 3.2→25 Å / Num. obs: 33187 / % possible obs: 62.05 % / Redundancy: 2 % / CC_1/2: 0.98 / Net I/σ(I): 15.11
Reflection shell	Resolution: 3.2→3.314 Å / Num. unique obs: 1016 / CC_1/2: 0.724

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.2→24.001 Å / Cor.coef. F_o:F_c: 0.903 / Cor.coef. F_o:F_c free: 0.84 / SU B: 21.452 / SU ML: 0.353 / Cross valid method: FREE R-VALUE / ESU R Free: 0.637
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2602	1609	4.848 %
R_work	0.2154	31578	-
all	0.218	-	-
obs	-	33187	62.136 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 75.25 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.629 Å²	0 Å²	2.586 Å²
2-	-	-0.433 Å²	0 Å²
3-	-	-	-0.836 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→24.001 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12830	0	139	36	13005

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	13334
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	12334
X-RAY DIFFRACTION	r_angle_refined_deg	1.466	1.639	18089
X-RAY DIFFRACTION	r_angle_other_deg	1.187	1.583	28429
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.735	5	1545
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.337	21.722	755
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.449	15	2175
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.481	15	85
X-RAY DIFFRACTION	r_chiral_restr	0.06	0.2	1705
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	14795
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3190
X-RAY DIFFRACTION	r_nbd_refined	0.223	0.2	2876
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.204	0.2	12647
X-RAY DIFFRACTION	r_nbtor_refined	0.179	0.2	6366
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	6092
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.178	0.2	378
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.102	0.2	12
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.778	0.2	38
X-RAY DIFFRACTION	r_nbd_other	0.439	0.2	50
X-RAY DIFFRACTION	r_mcbond_it	5.315	7.792	6195
X-RAY DIFFRACTION	r_mcbond_other	5.308	7.792	6194
X-RAY DIFFRACTION	r_mcangle_it	8.562	11.68	7735
X-RAY DIFFRACTION	r_mcangle_other	8.561	11.681	7736
X-RAY DIFFRACTION	r_scbond_it	5.003	8.418	7139
X-RAY DIFFRACTION	r_scbond_other	5.003	8.419	7140
X-RAY DIFFRACTION	r_scangle_it	8.438	12.457	10354
X-RAY DIFFRACTION	r_scangle_other	8.438	12.457	10355
X-RAY DIFFRACTION	r_lrange_it	12.959	88.806	14846
X-RAY DIFFRACTION	r_lrange_other	12.96	88.821	14843
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.039	0.05	10639
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.034	0.05	10653
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.028	0.05	10654
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.04	0.05	10634
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.043	0.05	10624
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.038	0.05	10652
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.045	0.05	10623
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.034	0.05	10613
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.041	0.05	10604
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.039	0.05	10629

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.2-3.282	0.301	36	0.311	670	X-RAY DIFFRACTION	18.3472
3.282-3.37	0.291	48	0.309	788	X-RAY DIFFRACTION	21.902
3.37-3.466	0.332	51	0.28	966	X-RAY DIFFRACTION	27.7566
3.466-3.57	0.273	43	0.249	1086	X-RAY DIFFRACTION	31.6512
3.57-3.685	0.296	59	0.259	1180	X-RAY DIFFRACTION	36.0804
3.685-3.811	0.307	63	0.241	1330	X-RAY DIFFRACTION	41.5449
3.811-3.952	0.297	76	0.237	1492	X-RAY DIFFRACTION	48.2759
3.952-4.109	0.286	88	0.245	1713	X-RAY DIFFRACTION	57.7059
4.109-4.286	0.283	97	0.225	2055	X-RAY DIFFRACTION	72.3118
4.286-4.489	0.278	108	0.231	2234	X-RAY DIFFRACTION	81.8595
4.489-4.723	0.231	129	0.194	2351	X-RAY DIFFRACTION	89.5954
4.723-4.999	0.263	117	0.2	2361	X-RAY DIFFRACTION	96.5329
4.999-5.329	0.253	117	0.208	2340	X-RAY DIFFRACTION	99.7969
5.329-5.734	0.253	116	0.203	2162	X-RAY DIFFRACTION	99.781
5.734-6.248	0.239	115	0.174	2005	X-RAY DIFFRACTION	99.9529
6.248-6.932	0.235	82	0.177	1859	X-RAY DIFFRACTION	100
6.932-7.904	0.216	89	0.154	1643	X-RAY DIFFRACTION	100
7.904-9.447	0.177	74	0.157	1416	X-RAY DIFFRACTION	100
9.447-12.497	0.177	55	0.169	1148	X-RAY DIFFRACTION	100
12.497-24.001	0.421	46	0.409	779	X-RAY DIFFRACTION	100

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