PDB-4twf: X-ray structure of a pentameric ligand gated ion channel from Erw...

ID or keywords:

Entry

Database: PDB / ID: 4twf

Title

X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) in complex with bromomemantine

Components

Cys-loop ligand-gated ion channel

Keywords

TRANSPORT PROTEIN / ELIC / LGIC / cys-loop / channel / memantine / pore blocker

Function / homology

Function and homology information

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

Biological species

Dickeya chrysanthemi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.901 Å

Authors

Ulens, C. / Spurny, R. / Thompson, A.J. / Alqazzaz, M. / Debaveye, S. / Lu, H. / Price, K. / Villalgordo, J.M. / Tresadern, G. / Lynch, J.W. / Lummis, S.C.R.

Citation

Journal: Structure / Year: 2014
Title: The Prokaryote Ligand-Gated Ion Channel ELIC Captured in a Pore Blocker-Bound Conformation by the Alzheimer's Disease Drug Memantine.
Authors: Ulens, C. / Spurny, R. / Thompson, A.J. / Alqazzaz, M. / Debaveye, S. / Han, L. / Price, K. / Villalgordo, J.M. / Tresadern, G. / Lynch, J.W. / Lummis, S.C.

History

Deposition	Jun 30, 2014	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Sep 24, 2014	Provider: repository / Type: Initial release
Revision 1.1	Oct 22, 2014	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4twf.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb4twf.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	4twf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4twf_validation.pdf.gz	3.5 MB	Display	wwPDB validaton report
Full document	4twf_full_validation.pdf.gz	3.7 MB	Display
Data in XML	4twf_validation.xml.gz	121.9 KB	Display
Data in CIF	4twf_validation.cif.gz	158 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tw/4twf ftp://data.pdbj.org/pub/pdb/validation_reports/tw/4twf	HTTPS FTP

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Related structure data

Related structure data	4twdC 4twhC 2vl0S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4twd-1 3uq5-2 3zkr-1 2vl0-1 3uq7-1 4a98-1 3uq5-1 4a98-2 4twd-2 3uq4-2 5heo-2 3uq4-1 3rqu-2 2yn6-d 4a97-1 4twh-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4twdC

4twhC

2vl0S

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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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

A: Cys-loop ligand-gated ion channel

B: Cys-loop ligand-gated ion channel

C: Cys-loop ligand-gated ion channel

D: Cys-loop ligand-gated ion channel

E: Cys-loop ligand-gated ion channel

F: Cys-loop ligand-gated ion channel

G: Cys-loop ligand-gated ion channel

H: Cys-loop ligand-gated ion channel

I: Cys-loop ligand-gated ion channel

J: Cys-loop ligand-gated ion channel

hetero molecules

356 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cys-loop ligand-gated ion channel

B: Cys-loop ligand-gated ion channel

C: Cys-loop ligand-gated ion channel

D: Cys-loop ligand-gated ion channel

E: Cys-loop ligand-gated ion channel

hetero molecules

defined by author&software
178 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Cys-loop ligand-gated ion channel

G: Cys-loop ligand-gated ion channel

H: Cys-loop ligand-gated ion channel

I: Cys-loop ligand-gated ion channel

J: Cys-loop ligand-gated ion channel

hetero molecules

defined by author&software
178 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	106.505, 266.092, 112.175
Angle α, β, γ (deg.)	90.00, 107.70, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Cys-loop ligand-gated ion channel / ELIC Mass: 35281.191 Da / Num. of mol.: 10 / Fragment: UNP residues 11-316 / Mutation: F246S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dickeya chrysanthemi (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P0C7B7
#2: Chemical	ChemComp-BR7 / Bromomemantine Mass: 258.198 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₂H₂₀BrN

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 4.29 Å³/Da / Density % sol: 71.34 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 200 mM ammonium sulphate, 50 mM ADA pH 5.5, 20 % PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.91946 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 10, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91946 Å / Relative weight: 1
Reflection	Resolution: 3.9→49.83 Å / Num. obs: 53624 / % possible obs: 99.3 % / Redundancy: 4.9 % / Net I/σ(I): 8.7
Reflection shell	Resolution: 3.9→4.11 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.936 / Num. unique all: 7432 / % possible all: 95.5

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
SCALA		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2vl0

2vl0

Resolution: 3.901→49.83 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.37 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2499	2718	5.08 %
R_work	0.2021	-	-
obs	0.2045	53548	99.22 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.901→49.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24970	0	168	0	25138

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	25832
X-RAY DIFFRACTION	f_angle_d	1.56	35310
X-RAY DIFFRACTION	f_dihedral_angle_d	15.548	9200
X-RAY DIFFRACTION	f_chiral_restr	0.066	3938
X-RAY DIFFRACTION	f_plane_restr	0.008	4460

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 (%)
3.9014-3.9724	0.3849	133	0.3186	2320	X-RAY DIFFRACTION	87
3.9724-4.0487	0.3713	137	0.2805	2708	X-RAY DIFFRACTION	100
4.0487-4.1313	0.275	140	0.2531	2681	X-RAY DIFFRACTION	100
4.1313-4.2211	0.3184	138	0.2395	2688	X-RAY DIFFRACTION	100
4.2211-4.3193	0.2613	144	0.2143	2708	X-RAY DIFFRACTION	100
4.3193-4.4272	0.2774	152	0.2088	2664	X-RAY DIFFRACTION	100
4.4272-4.5468	0.223	130	0.1879	2681	X-RAY DIFFRACTION	100
4.5468-4.6805	0.2604	148	0.1828	2708	X-RAY DIFFRACTION	100
4.6805-4.8315	0.2451	138	0.1757	2709	X-RAY DIFFRACTION	100
4.8315-5.004	0.2198	126	0.1833	2691	X-RAY DIFFRACTION	100
5.004-5.2042	0.2744	147	0.1753	2689	X-RAY DIFFRACTION	100
5.2042-5.4407	0.2111	150	0.1777	2692	X-RAY DIFFRACTION	100
5.4407-5.7272	0.2318	142	0.1756	2684	X-RAY DIFFRACTION	100
5.7272-6.0854	0.2598	146	0.18	2700	X-RAY DIFFRACTION	100
6.0854-6.5544	0.2831	169	0.1994	2683	X-RAY DIFFRACTION	100
6.5544-7.2122	0.2586	156	0.1921	2688	X-RAY DIFFRACTION	100
7.2122-8.2517	0.2191	155	0.1789	2692	X-RAY DIFFRACTION	100
8.2517-10.3808	0.1827	148	0.1613	2697	X-RAY DIFFRACTION	100
10.3808-49.838	0.2597	119	0.2488	2747	X-RAY DIFFRACTION	99

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.5712	0.1795	0.0539	2.6615	2.6286	6.986	-0.1232	-0.2463	-0.1781	0.6742	-0.2035	0.879	0.7003	-0.5677	0.0507	0.7798	-0.0804	0.0636	0.8921	0.0464	0.9341	-125.4088	-49.3244	-44.9559
2	0.5501	-0.3612	0.1399	2.7519	2.2074	5.8036	-0.0723	-0.0896	-0.1284	0.1918	0.1071	-0.0238	0.1562	0.1124	0.0365	0.9176	0.0157	0.1204	0.524	-0.0075	0.8188	-104.8676	-61.078	-40.8497
3	1.1657	0.09	-2.0658	0.878	0.4629	7.795	-0.056	-0.1003	-0.1302	-0.0599	0.1143	-0.6048	0.6129	0.4547	-0.3903	0.7886	0.1947	0.0399	0.5375	0.0297	0.9136	-86.6207	-45.6265	-43.1651
4	1.1055	-0.3035	-0.0738	0.981	1.091	7.0075	0.1309	-0.2058	0.2277	-0.1081	-0.071	-0.3587	0.6626	0.1326	-0.4245	1.0474	0.024	0.3472	0.6874	-0.0027	0.9047	-95.8336	-23.8998	-48.5591
5	0.9173	-0.0861	0.7614	1.7031	0.8362	8.2203	-0.089	0.0855	0.1208	0.0085	-0.0087	0.2791	-0.8853	-0.1491	0.1246	0.835	0.1121	0.1376	0.8326	0.2401	0.6734	-119.9088	-26.2105	-49.6554
6	8.1398	1.6283	-0.3525	1.3817	0.001	1.1538	0.102	-0.7511	0.5905	0.577	-0.1459	-0.1559	0.0556	-0.1229	0.1482	0.8952	0.0248	0.1155	0.7916	-0.0363	1.0968	-82.4367	-117.4683	-18.2874
7	6.6129	2.7303	0.6745	2.0115	0.4567	0.7601	-0.2476	0.204	-0.5336	-0.1877	0.1798	-0.2519	0.1801	0.2317	0.1331	0.9717	0.0333	0.2654	0.6113	-0.0196	0.903	-78.7936	-127.9923	-39.7293
8	7.2642	0.0095	1.7467	1.3789	-0.1278	1.0651	0.0562	0.6679	-0.5935	-0.2925	0.0831	-0.3317	0.0173	0.3446	0.0382	1.0464	-0.0739	0.2017	0.5426	-0.183	1.1167	-81.6389	-111.5497	-57.0961
9	7.4381	1.9298	0.1826	0.8483	0.2423	1.1296	-0.3116	-0.0328	-1.0093	-0.3629	0.2485	-0.5162	-0.2737	0.146	0.2548	0.86	-0.0237	0.0432	0.5584	-0.0335	1.1724	-86.984	-90.4402	-46.3546
10	5.7212	0.1666	-0.5703	1.3004	-0.3424	0.9403	-0.1055	-0.5806	0.596	0.5201	0.057	0.072	-0.1034	0.0184	0.009	0.7894	0.1421	-0.003	0.815	-0.2481	1.2423	-87.5996	-94.2477	-22.402

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain E
6	X-RAY DIFFRACTION	6	chain F
7	X-RAY DIFFRACTION	7	chain G
8	X-RAY DIFFRACTION	8	chain H
9	X-RAY DIFFRACTION	9	chain I
10	X-RAY DIFFRACTION	10	chain J

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