PDB-5heh: Pentameric ligand-gated ion channel GLIC mutant P246A

ID or keywords:

Entry

Database: PDB / ID: 5heh

Title

Pentameric ligand-gated ion channel GLIC mutant P246A

Components

Proton-gated ion channel

Keywords

TRANSPORT PROTEIN / Pentameric ligand-gated ion channels / Membrane protein / Ligand-gated ion channel

Function / homology

Function and homology information

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

Biological species

Gloeobacter violaceus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.3 Å

Authors

Bertozzi, C. / Dutzler, R.

Citation

Journal: Plos Biol. / Year: 2016
Title: Signal Transduction at the Domain Interface of Prokaryotic Pentameric Ligand-Gated Ion Channels.
Authors: Bertozzi, C. / Zimmermann, I. / Engeler, S. / Hilf, R.J. / Dutzler, R.

History

Deposition	Jan 6, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Mar 2, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 16, 2016	Group: Database references
Revision 1.2	Jan 10, 2024	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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Download

PDBx/mmCIF format	5heh.cif.gz	632.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5heh.ent.gz	536 KB	Display	PDB format
PDBx/mmJSON format	5heh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5heh_validation.pdf.gz	466.1 KB	Display	wwPDB validaton report
Full document	5heh_full_validation.pdf.gz	490.8 KB	Display
Data in XML	5heh_validation.xml.gz	52.9 KB	Display
Data in CIF	5heh_validation.cif.gz	70 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/he/5heh ftp://data.pdbj.org/pub/pdb/validation_reports/he/5heh	HTTPS FTP

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Related structure data

Related structure data	5hegC 5hejC 5heoC 5heuC 5hewC 3ehzS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6emx-d 5v6o-d 2xq5-d 3ehz-d 2xq4-d 5heg-d 2xq9-d 4zzb-d 3p50-d 3eam-d 2xq7-d 6f0z-d 6f0m-d 6f0i-d 6hja-d 4il4-d 4ilb-d 6hya-d 4ire-d 6f13-d 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 (7) #71 - Nov 2005 Acetylcholine Receptor similarity (5)

Deposited unit

A: Proton-gated ion channel

B: Proton-gated ion channel

C: Proton-gated ion channel

D: Proton-gated ion channel

E: Proton-gated ion channel

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	177.690, 133.940, 159.830
Angle α, β, γ (deg.)	90.00, 101.10, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	Proton-gated ion channel / GLIC / Ligand-gated ion channel / LGIC Mass: 36194.637 Da / Num. of mol.: 5 / Mutation: P246A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gloeobacter violaceus (bacteria) / Gene: glvI, glr4197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7NDN8

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 5.16 Å³/Da / Density % sol: 76.15 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: PEG 4000, Ammonium Sulfate

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9197 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9197 Å / Relative weight: 1
Reflection	Resolution: 3.3→50 Å / Num. obs: 55197 / % possible obs: 99.6 % / Redundancy: 5.3 % / R_merge(I) obs: 0.101 / Net I/σ(I): 13.1
Reflection shell	Resolution: 3.3→3.4 Å / Redundancy: 5.4 % / R_merge(I) obs: 0.773 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3EHZ

3ehz

Resolution: 3.3→29.913 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2803	2794	5.07 %
R_work	0.2438	-	-
obs	0.2457	55058	99.5 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.3→29.913 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12595	0	0	0	12595

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	12930
X-RAY DIFFRACTION	f_angle_d	0.654	17660
X-RAY DIFFRACTION	f_dihedral_angle_d	15.128	7640
X-RAY DIFFRACTION	f_chiral_restr	0.043	2060
X-RAY DIFFRACTION	f_plane_restr	0.004	2210

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 (%)
3.3-3.3568	0.3996	187	0.3582	2559	X-RAY DIFFRACTION	100
3.3568-3.4178	0.4056	100	0.3464	2644	X-RAY DIFFRACTION	100
3.4178-3.4834	0.3943	96	0.3346	2657	X-RAY DIFFRACTION	99
3.4834-3.5544	0.3515	178	0.3134	2517	X-RAY DIFFRACTION	100
3.5544-3.6316	0.3359	181	0.3002	2562	X-RAY DIFFRACTION	99
3.6316-3.7159	0.3221	102	0.2933	2675	X-RAY DIFFRACTION	100
3.7159-3.8087	0.3232	84	0.2677	2643	X-RAY DIFFRACTION	100
3.8087-3.9114	0.3567	187	0.2704	2541	X-RAY DIFFRACTION	100
3.9114-4.0263	0.3395	187	0.2717	2578	X-RAY DIFFRACTION	100
4.0263-4.1559	0.3254	69	0.2489	2677	X-RAY DIFFRACTION	100
4.1559-4.304	0.2938	118	0.242	2638	X-RAY DIFFRACTION	100
4.304-4.4758	0.2905	187	0.2229	2575	X-RAY DIFFRACTION	100
4.4758-4.6788	0.2058	187	0.1929	2554	X-RAY DIFFRACTION	100
4.6788-4.9244	0.2815	50	0.1784	2693	X-RAY DIFFRACTION	100
4.9244-5.2314	0.2421	136	0.1902	2637	X-RAY DIFFRACTION	100
5.2314-5.6329	0.2507	187	0.2376	2581	X-RAY DIFFRACTION	100
5.6329-6.1952	0.3071	187	0.2525	2566	X-RAY DIFFRACTION	99
6.1952-7.0812	0.2738	6	0.243	2758	X-RAY DIFFRACTION	100
7.0812-8.8827	0.3093	181	0.218	2584	X-RAY DIFFRACTION	99
8.8827-29.9139	0.1969	184	0.235	2625	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	0.6101	-0.2731	-0.4198	0.0175	0.2505	0.1622	-0.1653	0.1249	0.4486	0.067	-0.2859	0.317	-0.0002	0.2013	-0.0123	0.7766	-0.0981	0.0682	0.5389	-0.0294	0.4129	21.0313	-4.4525	84.5042
2	0.5276	0.2976	0.1184	1.2355	-0.0291	0.4042	0.2297	-0.1328	-0.2614	0.3226	0.0365	-0.0615	0.1762	-0.3194	-0.0003	0.429	-0.0412	0.0268	0.4921	-0.0007	0.4729	8.6017	-7.4805	56.7556
3	0.0798	-0.35	-0.0788	0.1442	0.0934	0.0932	0.1403	0.095	-0.3483	-0.2841	-0.0529	0.3678	-0.3036	-0.7821	-0	0.631	-0.0061	0.0025	0.8319	-0.0832	0.6444	-3.5135	-12.4918	29.0276
4	0.2201	-0.0446	0.2557	0.3865	-0.0946	0.1619	-0.0391	-0.1798	0.0913	0.3192	-0.2762	0.042	-0.0192	0.0788	0	0.5865	0.1017	0.1648	0.5781	-0.0335	0.4698	22.1392	19.467	75.9884
5	0.0558	-0.0629	-0.0278	0.0507	0.0053	0.0439	-0.0994	-0.4361	-0.1955	0.6807	0.6491	0.0885	0.0344	0.3136	0.0002	1.2727	0.1787	-0.3437	1.2356	-0.2183	0.8515	35.1346	28.6008	97.808
6	0.1868	-0.0156	-0.0069	0.0249	-0.0704	0.0786	-0.4748	0.016	-0.0123	0.5812	0.3142	-0.0083	0.1909	0.7002	-0.0001	0.7404	0.1092	0.0368	0.7063	-0.1279	0.5313	28.7256	17.6696	80.8124
7	0.4022	-0.4043	0.0541	0.3646	0.2536	0.4743	-0.3864	-0.3179	0.2435	-0.0788	-0.3087	-0.1343	-0.4446	-0.347	-0.0292	0.5129	-0.0651	-0.0341	0.3795	0.0099	0.4591	15.5023	20.7672	69.6739
8	0.2711	-0.1549	-0.0868	0.1594	0.1711	0.1726	0.107	-0.3256	0.1812	-0.4232	-0.1947	-0.1448	0.0332	-0.3455	0.0001	0.9288	-0.1784	-0.098	0.8091	0.0468	0.6423	12.2843	19.0998	75.435
9	0.1499	0.008	0.0108	0.3483	0.1391	0.0496	-0.0909	-0.0107	-0.3208	-0.1986	0.4824	0.2864	0.3353	-0.162	0.3867	1.4415	-0.5895	-0.442	-0.037	-0.0256	0.6516	13.2952	21.503	59.6379
10	0.4713	0.0354	-0.6338	0.3806	-0.015	0.6134	-0.2319	0.0701	0.0437	0.1654	-0.048	-0.1579	-0.1542	-0.0697	0	0.6347	-0.0096	-0.0578	0.6981	0.0174	0.6812	0.9072	10.6818	31.062
11	0.122	0.3288	-0.1553	0.4437	-0.313	0.172	-0.0356	0.4798	-0.2499	-0.6053	0.1931	0.7159	0.4101	-0.5851	0.0214	0.6433	0.5332	-0.0463	1.1357	-0.4073	0.8486	-8.1767	19.5238	33.5576
12	0.5588	-0.1911	0.0907	0.0463	-0.0485	0.0316	0.0064	-0.2789	0.408	-0.1256	-0.1293	0.1684	0.3377	-0.1253	-0.0001	0.5722	-0.1272	-0.1217	0.5884	0.0035	0.6406	45.0947	23.1711	63.9322
13	0.3896	-0.2711	0.0339	0.2111	-0.0676	0.119	-0.1555	-0.2248	0.1373	0.1083	0.1326	0.0283	-0.553	-0.0493	0.0011	1.1015	0.5682	-0.6281	1.438	-0.6363	1.6053	64.8588	24.7526	82.2113
14	0.0556	-0.2001	-0.0736	0.2916	0.3131	0.1489	0.1809	-0.1328	0.1991	-0.3211	-0.0259	-0.0228	0.2737	-0.2248	-0.0001	0.6983	0.104	-0.1973	0.5376	-0.1084	0.7181	47.9366	19.2393	70.7444
15	2.17	-0.6186	-1.1071	0.2608	0.6975	1.6224	-0.7027	0.6411	1.0992	0.3115	-0.3573	-0.6627	-1.0168	-0.1347	-0.804	0.3748	-0.3048	-0.0444	-0.244	0.2025	0.5226	41.3921	26.3453	56.0858
16	0.1508	-0.0839	0.1619	0.3356	-0.1501	0.1584	-0.2201	0.0572	0.0398	-0.2855	0.0881	0.0059	-0.0428	-0.0174	0	0.8628	-0.15	0.0414	0.5887	0.0344	0.6387	40.1283	31.1044	60.7687
17	0.048	0.0281	0.1298	-0.0295	0.1076	0.1292	0.0584	0.0509	-0.1524	0.0348	0.0342	-0.2103	-0.3742	0.0945	0.3264	-0.2115	0.0078	0.8373	0.6446	-0.1036	0.0788	38.145	23.9522	46.603
18	0.643	0.1518	-0.4148	0.724	-0.1608	0.2561	-0.1014	0.5192	0.0935	-0.5909	-0.1618	0.272	-0.5387	0.2315	-0.0031	0.6547	0.0011	-0.0517	0.7486	0.1006	0.6081	15.3121	18.3509	23.5055
19	0.993	-0.415	-0.9806	0.1625	0.4066	0.9927	0.574	-0.0877	-0.0671	-2.0143	0.7912	0.9585	0.4254	-0.1116	0.7697	1.4541	-0.1289	-0.6363	0.7933	0.2631	0.8939	19.3379	29.8229	19.0903
20	0.3792	-0.1773	-0.2357	-0.1655	0.0882	0.6307	-0.0557	0.091	-0.1495	-0.1112	0.0091	0.1145	-0.0996	-0.3236	-0	0.446	0.003	-0.0654	0.4431	-0.0279	0.5262	57.0077	-2.2174	65.8858
21	0.5161	-0.1079	0.3745	-0.5619	0.0874	0.1697	0.4084	0.4239	0.0374	-0.556	-0.1888	0.083	0.2899	0.3953	-0.0059	0.6134	0.0299	-0.0502	0.54	-0.0033	0.5842	43.7401	1.2879	38.6044
22	0.334	0.0821	-0.3528	0.0958	-0.0416	0.3421	-0.2055	0.5563	-0.0155	-0.2716	0.0009	0.0502	-0.2361	0.5398	-0.0001	0.6345	-0.0532	0.0471	0.8019	0.0264	0.5199	31.3823	6.5343	11.007
23	0.0141	0.0963	0.1014	0.0743	-0.0285	0.5946	-0.1742	-0.3954	0.1095	0.0159	-0.1219	0.0692	-0.2311	-0.5192	-0.0057	0.6844	-0.0697	-0.0969	0.3736	0.0538	0.4651	38.2118	-18.7966	67.5098
24	0.2258	0.1017	-0.0432	0.5091	0.2279	0.1532	0.0552	-0.4999	-0.6339	0.3	0.5188	-0.4606	0.1296	-0.3906	0.1007	1.3719	-0.4786	-0.4638	1.0452	0.4052	0.8555	44.0045	-25.3762	93.0254
25	0.1039	-0.0802	-0.0156	-0.0079	0.0256	0.0492	0.0996	-0.0341	0.1741	0.1158	0.0358	-0.3078	0.1738	-0.1886	0	0.7052	-0.0607	-0.148	0.5264	0.0258	0.6607	39.9426	-15.2309	74.8762
26	0.688	-0.2334	-0.0185	0.152	-0.0764	0.1306	0.472	0.4666	-0.3596	-0.2468	-0.235	-0.7131	0.5199	-0.0396	-0.009	0.6869	-0.026	-0.1875	0.4079	0.0018	0.6272	34.9117	-19.6013	50.4553
27	0.4205	0.1017	-0.2701	0.1111	0.106	0.6213	0.0577	0.0914	0.4061	1.017	-0.1032	-0.3391	0.7939	0.1772	-0.0441	1.0283	0.0081	-0.2354	0.4383	-0.1478	0.8738	36.4201	-23.4814	67.4221
28	0.1289	-0.1531	-0.202	0.2325	0.5068	1.4305	0.1713	0.2571	0.6143	-0.3484	0.2947	0.3325	0.3163	0.4988	0.0201	0.9774	-0.019	-0.3945	0.5357	0.0656	0.9562	42.1556	-23.5036	59.7764
29	1.8201	0.5196	-0.4507	0.4576	-0.3272	0.2277	0.2736	0.3864	-0.3904	0.2786	0.2879	-0.3561	0.4688	0.0568	0.7659	0.8107	-0.177	-0.3347	0.5531	0.0368	0.8083	28.8214	-20.5411	51.435
30	0.0752	0.2071	-0.0313	0.2362	-0.353	0.1711	0.2537	0.3622	0.0762	-0.274	-0.0228	0.3008	0.3689	-0.034	-0	0.6498	0.0514	0.0349	0.7706	-0.0062	0.5104	18.6858	-10.3977	21.7554
31	0.2987	-0.1238	-0.2184	0.0184	0.0073	0.1494	-0.1606	0.0783	0.04	-0.4468	-0.3792	0.57	-0.2365	0.4204	-0.0002	0.908	-0.0706	-0.2525	0.5571	-0.0783	0.8079	19.703	-22.9796	18.935

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 11 through 114 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 115 through 256 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 257 through 320 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 11 through 51 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 52 through 66 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 67 through 114 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 115 through 162 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 163 through 182 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 183 through 204 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 205 through 287 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 288 through 320 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 11 through 51 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 52 through 66 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 67 through 114 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 115 through 162 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 163 through 182 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 183 through 204 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 205 through 287 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 288 through 320 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 11 through 114 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 115 through 256 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 257 through 320 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 11 through 51 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 52 through 66 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 67 through 114 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 115 through 136 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 137 through 162 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 163 through 182 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 183 through 204 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 205 through 287 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 288 through 320 )

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About Yorodumi

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Yorodumi