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

ID or keywords:

Entry

Database: PDB / ID: 4twh

Title

X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) mutant F16'S

Components

Cys-loop ligand-gated ion channel

Keywords

TRANSPORT PROTEIN / ELIC /

LGIC /

cys-loop / channel

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: 3.6 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	4twh.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb4twh.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	4twh.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/tw/4twh ftp://data.pdbj.org/pub/pdb/validation_reports/tw/4twh	HTTPS FTP

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Related structure data

Related structure data	4twdC 4twfC 2vl0S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3zkr-2 2yoe-1 3uq7-2 4z90-1 4a97-1 2yoe-2 2vl0-2 5sxv-1 3zkr-1 4a97-2 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

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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

353 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

defined by author&software
176 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

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

Unit cell

Length a, b, c (Å)	105.901, 264.974, 111.329
Angle α, β, γ (deg.)	90.00, 108.82, 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

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 4.19 Å³/Da / Density % sol: 70.65 %
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: Mar 30, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9999 Å / Relative weight: 1
Reflection	Resolution: 3.6→48.96 Å / Num. obs: 66992 / % possible obs: 99.9 % / Redundancy: 3.9 % / Net I/σ(I): 8.4
Reflection shell	Resolution: 3.6→3.79 Å / Redundancy: 4 % / R_merge(I) obs: 0.993 / Num. unique all: 9751 / % possible all: 99.3

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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: 3.6→48.624 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.06 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2634	3360	5.02 %
R_work	0.2201	-	-
obs	0.2224	66917	99.86 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.6→48.624 Å

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

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	25640
X-RAY DIFFRACTION	f_angle_d	1.589	34950
X-RAY DIFFRACTION	f_dihedral_angle_d	15.525	9200
X-RAY DIFFRACTION	f_chiral_restr	0.065	3890
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 (%)
3.6-3.6515	0.3624	133	0.3265	2637	X-RAY DIFFRACTION	100
3.6515-3.7059	0.3462	123	0.3084	2673	X-RAY DIFFRACTION	100
3.7059-3.7638	0.3609	118	0.3049	2657	X-RAY DIFFRACTION	100
3.7638-3.8255	0.3609	130	0.2909	2638	X-RAY DIFFRACTION	100
3.8255-3.8914	0.3017	134	0.2711	2640	X-RAY DIFFRACTION	100
3.8914-3.9622	0.2876	138	0.2553	2684	X-RAY DIFFRACTION	100
3.9622-4.0383	0.2632	147	0.2406	2597	X-RAY DIFFRACTION	100
4.0383-4.1207	0.3146	123	0.2325	2676	X-RAY DIFFRACTION	100
4.1207-4.2103	0.2904	125	0.2276	2658	X-RAY DIFFRACTION	100
4.2103-4.3082	0.253	131	0.2171	2656	X-RAY DIFFRACTION	100
4.3082-4.4158	0.2604	158	0.2058	2639	X-RAY DIFFRACTION	100
4.4158-4.5351	0.2394	128	0.1931	2657	X-RAY DIFFRACTION	100
4.5351-4.6685	0.2362	157	0.1848	2632	X-RAY DIFFRACTION	100
4.6685-4.8191	0.2586	137	0.1773	2653	X-RAY DIFFRACTION	100
4.8191-4.9911	0.2366	151	0.1907	2607	X-RAY DIFFRACTION	100
4.9911-5.1907	0.2284	162	0.1771	2632	X-RAY DIFFRACTION	100
5.1907-5.4267	0.256	135	0.1806	2646	X-RAY DIFFRACTION	100
5.4267-5.7124	0.2071	154	0.1962	2636	X-RAY DIFFRACTION	100
5.7124-6.0697	0.2547	158	0.2021	2667	X-RAY DIFFRACTION	100
6.0697-6.5373	0.3079	151	0.2172	2646	X-RAY DIFFRACTION	100
6.5373-7.1933	0.2877	147	0.2241	2627	X-RAY DIFFRACTION	100
7.1933-8.2298	0.2965	125	0.2105	2676	X-RAY DIFFRACTION	100
8.2298-10.3522	0.1962	152	0.1759	2651	X-RAY DIFFRACTION	99
10.3522-48.6283	0.2736	143	0.262	2672	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	0.1289	0.0693	0.1966	2.6915	2.2748	9.0783	0.1778	-0.0957	-0.2537	0.5073	-0.0622	0.5899	0.2251	-0.9604	0.0141	0.7133	-0.0325	0.184	0.7258	0.0822	0.8237	-124.09	-50.9696	-45.2405
2	0.6973	-0.7495	-0.7671	2.0806	2.2114	6.8989	0.0594	-0.0895	-0.163	0.0012	0.0396	-0.071	-0.0711	-0.1557	0.0321	0.9556	-0.0303	0.149	0.4583	-0.0005	0.7602	-103.8276	-63.0373	-40.847
3	0.949	0.0604	-1.6875	1.2528	0.7254	7.3166	0.1372	-0.0549	-0.0196	-0.1159	0.1598	-0.5369	0.2983	0.6188	-0.1797	0.6182	0.1611	0.0064	0.445	0.0239	0.8036	-85.3559	-47.8887	-42.7416
4	0.9159	-0.5227	-0.9812	1.2419	1.3528	8.8566	0.0272	-0.1906	0.3379	-0.1676	0.084	-0.4534	0.2336	0.3901	-0.2536	0.8659	0.0196	0.2432	0.4987	0.0232	0.9419	-94.1137	-26.2127	-48.2786
5	0.8012	0.085	0.403	1.1272	1.3297	4.9236	0.0723	-0.09	0.139	0.0704	0.0381	0.208	-0.3745	-0.1505	-0.2598	0.9677	0.149	0.2004	0.7075	0.1753	0.7097	-118.1097	-28.1671	-49.9185
6	8.3218	1.7581	-0.0385	1.7929	0.3278	1.3277	0.1296	-0.682	0.4904	0.5141	-0.0688	0.0768	0.0953	-0.0167	0.0244	0.8059	0.0931	0.1416	0.5853	0.0212	0.7059	-81.914	-119.0447	-17.6145
7	7.5869	3.0255	1.1247	1.6523	0.3704	0.5364	-0.1119	-0.1155	-0.302	-0.0003	0.0116	-0.1726	0.2291	0.1537	0.0257	0.846	0.0041	0.2644	0.5309	-0.0018	1.0488	-78.068	-129.8295	-38.8452
8	8.331	0.7591	1.6223	1.3051	0.1878	0.9594	-0.1353	0.5506	-0.5262	-0.2613	0.1143	-0.2706	0.1177	0.1848	-0.1254	1.0364	-0.0835	0.2204	0.4301	-0.0401	0.7941	-80.5934	-113.4583	-56.259
9	7.9132	1.1765	0.6896	1.4615	0.2652	0.8267	-0.4222	0.1273	-0.0246	-0.2774	0.2594	-0.3785	-0.116	0.2213	0.1862	0.7769	0.0127	0.0809	0.5007	0.0672	0.942	-86.1107	-92.494	-45.8805
10	8.7982	1.7028	-1.1469	1.1475	-0.3927	1.1343	-0.3944	-0.5116	0.3193	0.2658	0.133	0.1599	-0.0072	-0.0107	0.1669	0.7274	0.1402	0.0119	0.6176	-0.1791	1.0466	-87.0082	-96.0464	-21.9905

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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