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

ID or keywords:

Entry

Database: PDB / ID: 4twd

Title

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

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 / regulation of membrane potential / transmembrane signaling receptor activity / neuron projection / signal transduction / identical protein binding / plasma membrane
Similarity search - Function

Biological species

Dickeya chrysanthemi (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / AB INITIO PHASING / Resolution: 3.2 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	4twd.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb4twd.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	4twd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4twd_validation.pdf.gz	555 KB	Display	wwPDB validaton report
Full document	4twd_full_validation.pdf.gz	671.4 KB	Display
Data in XML	4twd_validation.xml.gz	114 KB	Display
Data in CIF	4twd_validation.cif.gz	150 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tw/4twd ftp://data.pdbj.org/pub/pdb/validation_reports/tw/4twd	HTTPS FTP

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Related structure data

Related structure data	4twfC 4twhC 2vl0S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4twf-1 3zkr-1 3uq5-2 3uq5-1 3uq7-1 2vl0-1 3uq4-2 3uq4-1 4a98-2 3rqu-2 5heo-2 4z91-2 4a98-1 5hew-2 2yks-1 5lid-1 3rqw-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

4twfC

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

355 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
177 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
177 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	105.482, 265.284, 111.098
Angle α, β, γ (deg.)	90.00, 110.28, 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 / Mutation: F16S 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-377 / Memantine Mass: 179.302 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₂H₂₁N / Comment: medication*YM

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 4.13 Å³/Da / Density % sol: 70.24 %
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: 0.9999 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 25, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9999 Å / Relative weight: 1
Reflection	Resolution: 3.2→49.47 Å / Num. obs: 93823 / % possible obs: 99.8 % / Redundancy: 3.5 % / Net I/σ(I): 12.5
Reflection shell	Resolution: 3.2→3.37 Å / Redundancy: 3.3 % / R_merge(I) obs: 1.5 / Num. unique all: 13615 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8_1069)	refinement
SCALA		data scaling
XDS		data reduction

Refinement

Method to determine structure: AB INITIO PHASING
Starting model: 2vl0

2vl0

Resolution: 3.2→48.634 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.31 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2522	4703	5.02 %
R_work	0.199	-	-
obs	0.2017	93729	99.75 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.2→48.634 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24970	0	156	0	25126

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	25820
X-RAY DIFFRACTION	f_angle_d	1.71	35274
X-RAY DIFFRACTION	f_dihedral_angle_d	17.312	9200
X-RAY DIFFRACTION	f_chiral_restr	0.107	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 (%)
3.2001-3.2365	0.378	137	0.329	2930	X-RAY DIFFRACTION	99
3.2365-3.2746	0.3769	157	0.3276	2959	X-RAY DIFFRACTION	100
3.2746-3.3145	0.3531	140	0.3107	2949	X-RAY DIFFRACTION	100
3.3145-3.3564	0.3518	158	0.2964	3014	X-RAY DIFFRACTION	100
3.3564-3.4006	0.3098	145	0.2774	2972	X-RAY DIFFRACTION	100
3.4006-3.4472	0.2938	134	0.2625	2965	X-RAY DIFFRACTION	100
3.4472-3.4964	0.3248	156	0.2489	2973	X-RAY DIFFRACTION	100
3.4964-3.5486	0.313	148	0.2555	2971	X-RAY DIFFRACTION	100
3.5486-3.604	0.3119	165	0.2476	2958	X-RAY DIFFRACTION	100
3.604-3.6631	0.3033	152	0.2319	2966	X-RAY DIFFRACTION	100
3.6631-3.7262	0.2837	155	0.2161	2981	X-RAY DIFFRACTION	100
3.7262-3.7939	0.2658	158	0.2087	2976	X-RAY DIFFRACTION	100
3.7939-3.8669	0.2758	178	0.2023	2940	X-RAY DIFFRACTION	100
3.8669-3.9458	0.2714	165	0.1897	2961	X-RAY DIFFRACTION	100
3.9458-4.0315	0.2457	165	0.1836	2953	X-RAY DIFFRACTION	100
4.0315-4.1253	0.246	156	0.1741	2991	X-RAY DIFFRACTION	100
4.1253-4.2284	0.2176	164	0.17	2955	X-RAY DIFFRACTION	100
4.2284-4.3426	0.1852	139	0.1603	2940	X-RAY DIFFRACTION	100
4.3426-4.4703	0.2183	171	0.1408	2971	X-RAY DIFFRACTION	100
4.4703-4.6145	0.2049	169	0.1435	2985	X-RAY DIFFRACTION	100
4.6145-4.7793	0.1645	141	0.1373	2985	X-RAY DIFFRACTION	100
4.7793-4.9705	0.2414	155	0.1544	2951	X-RAY DIFFRACTION	100
4.9705-5.1964	0.2258	178	0.1599	2941	X-RAY DIFFRACTION	100
5.1964-5.4701	0.2163	159	0.1591	2960	X-RAY DIFFRACTION	100
5.4701-5.8123	0.2242	162	0.1701	2991	X-RAY DIFFRACTION	100
5.8123-6.2602	0.2386	149	0.1805	2984	X-RAY DIFFRACTION	100
6.2602-6.8886	0.2742	183	0.2085	2963	X-RAY DIFFRACTION	100
6.8886-7.8817	0.2686	172	0.1943	2963	X-RAY DIFFRACTION	100
7.8817-9.9163	0.1996	144	0.1803	3001	X-RAY DIFFRACTION	100
9.9163-48.6397	0.2949	148	0.2661	2977	X-RAY DIFFRACTION	98

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	0.4918	-0.1614	-0.2287	2.5485	1.8785	5.4581	0.169	-0.038	-0.1257	0.3111	-0.1022	0.6053	0.13	-0.8964	0.0725	0.7218	-0.0757	0.1239	0.7894	0.0221	0.8199	-122.5273	-50.5395	-44.8272
2	0.6691	-0.2473	-0.4423	2.2942	1.859	5.8823	-0.0122	-0.0216	-0.091	0.1392	0.0255	0.0373	0.3263	-0.143	0.0294	0.9758	0.0482	0.1219	0.4574	0.0178	0.7997	-102.4819	-62.7517	-39.9524
3	1.2797	-0.1867	-1.8414	1.2511	0.4292	7.1246	0.0173	-0.0927	0.013	-0.1269	0.0641	-0.4544	0.2526	0.7059	-0.1766	0.6465	0.0899	0.0324	0.4682	-0.0163	0.7984	-83.9206	-47.6493	-41.3503
4	0.776	-0.3501	-1.2339	0.7361	0.8878	5.4649	0.1643	-0.0929	0.1774	-0.1248	0.0884	-0.1964	-0.1821	0.3239	-0.2376	0.9706	0.0667	0.303	0.5629	-0.0212	0.9297	-92.3547	-25.8057	-46.9126
5	0.6958	0.1323	0.5789	1.566	0.412	6.6057	0.2344	-0.0092	0.2525	0.098	0.0379	0.2511	-0.9109	-0.5649	-0.2102	0.9022	0.1841	0.2045	0.7318	0.1252	0.8456	-116.3479	-27.6837	-49.0541
6	5.6014	1.0096	0.267	1.5081	0.114	1.1014	-0.034	-0.6496	0.0317	0.4339	-0.0129	-0.1504	0.0853	-0.1042	0.0232	0.8873	0.067	0.1357	0.6763	-0.0024	0.9297	-80.5633	-119.2087	-17.5019
7	6.9627	2.848	1.23	2.047	0.4587	0.9386	-0.2542	0.1021	-0.5166	-0.1806	0.1552	-0.18	0.1715	0.1462	0.0369	0.8896	0.0295	0.2532	0.5532	-0.0191	0.956	-76.8013	-129.6404	-38.9244
8	7.8579	0.5046	1.8122	1.4264	0.0105	1.1328	0.0111	0.6518	-0.4107	-0.345	0.0683	-0.2287	0.1159	0.1912	-0.1012	0.8923	-0.0759	0.2067	0.4952	-0.06	0.8695	-79.2663	-113.0286	-56.0894
9	8.103	1.4117	0.8188	1.4828	-0.0609	0.8498	-0.3159	0.1382	0.1879	-0.2826	0.1512	-0.4885	-0.1984	0.2028	0.1666	0.8114	0.0077	0.1282	0.4899	0.0145	1.0646	-84.7063	-92.1828	-45.2875
10	4.5891	0.7549	-0.6671	1.078	-0.6474	0.9502	-0.2692	-0.6099	0.4052	0.4785	0.0757	0.1886	-0.1534	-0.058	0.2116	0.934	0.119	0.0949	0.6958	-0.2428	1.1907	-85.5672	-96.0896	-21.4784

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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