PDB-4a97: X-ray structure of a pentameric ligand gated ion channel from Erw...

ID or keywords:

Entry

Database: PDB / ID: 4a97

Title

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

Components

CYS-LOOP LIGAND-GATED ION CHANNEL

Keywords

TRANSPORT PROTEIN /

CYS-LOOP RECEPTOR /

GABA-A RECEPTOR /

BENZODIAZEPINE

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

ERWINIA CHRYSANTHEMI (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.343 Å

Authors

Spurny, R. / Brams, M. / Ulens, C.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Pentameric Ligand-Gated Ion Channel Elic is Activated by Gaba and Modulated by Benzodiazepines.
Authors: Spurny, R. / Ramerstorfer, J. / Price, K. / Brams, M. / Ernst, M. / Nury, H. / Verheij, M. / Legrand, P. / Bertrand, D. / Bertrand, S. / Dougherty, D.A. / De Esch, I.J.P. / Corringer, P. / ...

History

Deposition	Nov 24, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 17, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 14, 2012	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4a97.cif.gz	1.2 MB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a9/4a97 ftp://data.pdbj.org/pub/pdb/validation_reports/a9/4a97	HTTPS FTP

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Related structure data

Related structure data	2yoeC 4a98C 2vl0S 2yks C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3rqu-1 4twh-2 2yoe-1 2yoe-2 2vl0-2 4a98-1 3rqu-2 3uq4-1 4twf-2 3zkr-1 3uq4-2 5lid-2 5heo-1 5hej-1 4a98-2 6v0b-d 3uq7-1 4twd-2 3uq5-2 4twf-1 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

C: citing same article (ref.)

S: Starting model for refinement

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

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

Unit cell

Length a, b, c (Å)	105.400, 266.830, 110.760
Angle α, β, γ (deg.)	90.00, 109.20, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	CYS-LOOP LIGAND-GATED ION CHANNEL / ELIC Mass: 35383.367 Da / Num. of mol.: 10 / Fragment: RESIDUES 11-316 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ERWINIA CHRYSANTHEMI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0C7B7
#2: Chemical	ChemComp-ZPC / (5R)-6-(5-chloropyridin-2-yl)-7-oxo-6,7-dihydro-5H-pyrrolo[3,4-b]pyrazin-5-yl 4-methylpiperazine-1-carboxylate / R-ZOPICLONE Mass: 388.808 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₁₇H₁₇ClN₆O₃

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 4.16 Å³/Da / Density % sol: 70.41 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 2, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9999 Å / Relative weight: 1
Reflection	Resolution: 3.34→43.95 Å / Num. obs: 83009 / % possible obs: 99.6 % / Observed criterion σ(I): 2.2 / Redundancy: 3.8 % / R_merge(I) obs: 0.11 / Net I/σ(I): 12.8

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.8_1069)	refinement
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VL0

2vl0

Resolution: 3.343→43.468 Å / SU ML: 0.5 / σ(F): 1.99 / Phase error: 28.85 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2587	4132	5 %
R_work	0.2053	-	-
obs	0.208	82811	99.45 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 3.343→43.468 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25020	0	270	0	25290

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	26000
X-RAY DIFFRACTION	f_angle_d	1.755	35460
X-RAY DIFFRACTION	f_dihedral_angle_d	18.646	9350
X-RAY DIFFRACTION	f_chiral_restr	0.12	3900
X-RAY DIFFRACTION	f_plane_restr	0.009	4500

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 (%)
3.3433-3.3813	0.3796	135	0.3169	2480	X-RAY DIFFRACTION	94
3.3813-3.4211	0.3548	135	0.308	2595	X-RAY DIFFRACTION	100
3.4211-3.4628	0.3759	141	0.2947	2651	X-RAY DIFFRACTION	100
3.4628-3.5066	0.3543	131	0.2756	2635	X-RAY DIFFRACTION	100
3.5066-3.5527	0.3446	132	0.2731	2607	X-RAY DIFFRACTION	100
3.5527-3.6013	0.3076	142	0.2679	2630	X-RAY DIFFRACTION	100
3.6013-3.6528	0.3627	118	0.3005	2583	X-RAY DIFFRACTION	98
3.6528-3.7073	0.4675	107	0.3333	2590	X-RAY DIFFRACTION	97
3.7073-3.7652	0.3053	142	0.246	2608	X-RAY DIFFRACTION	100
3.7652-3.8269	0.2802	143	0.2276	2657	X-RAY DIFFRACTION	100
3.8269-3.8928	0.2949	125	0.2291	2623	X-RAY DIFFRACTION	100
3.8928-3.9635	0.3035	149	0.224	2584	X-RAY DIFFRACTION	100
3.9635-4.0397	0.3034	139	0.2083	2677	X-RAY DIFFRACTION	100
4.0397-4.1221	0.2264	137	0.2033	2597	X-RAY DIFFRACTION	100
4.1221-4.2117	0.2628	153	0.1907	2641	X-RAY DIFFRACTION	100
4.2117-4.3096	0.2359	136	0.1733	2620	X-RAY DIFFRACTION	100
4.3096-4.4172	0.2261	138	0.167	2660	X-RAY DIFFRACTION	100
4.4172-4.5366	0.2274	141	0.1608	2606	X-RAY DIFFRACTION	100
4.5366-4.6699	0.194	136	0.149	2611	X-RAY DIFFRACTION	100
4.6699-4.8204	0.2054	142	0.1477	2675	X-RAY DIFFRACTION	100
4.8204-4.9925	0.2045	143	0.1526	2615	X-RAY DIFFRACTION	100
4.9925-5.1921	0.2112	142	0.1541	2618	X-RAY DIFFRACTION	100
5.1921-5.428	0.2373	144	0.1581	2615	X-RAY DIFFRACTION	100
5.428-5.7135	0.245	136	0.1681	2648	X-RAY DIFFRACTION	100
5.7135-6.0706	0.2143	166	0.1702	2615	X-RAY DIFFRACTION	100
6.0706-6.5379	0.2582	133	0.1873	2680	X-RAY DIFFRACTION	100
6.5379-7.1932	0.2663	126	0.2006	2609	X-RAY DIFFRACTION	100
7.1932-8.2279	0.2365	126	0.1768	2665	X-RAY DIFFRACTION	100
8.2279-10.3432	0.1744	161	0.1635	2639	X-RAY DIFFRACTION	100
10.3432-43.4713	0.2989	133	0.2717	2645	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	0.3613	-0.2204	-0.2004	1.2625	0.8991	5.9875	0.0343	-0.0772	-0.1126	0.4891	0.0566	0.4367	0.5495	-0.8185	-0.0912	0.7746	-0.1105	0.1041	0.8263	0.1041	0.8866	-123.2895	-49.1476	-43.8054
2	0.7838	-0.1624	-0.2495	2.3249	1.2392	4.0914	-0.0128	-0.1551	-0.1238	0.0592	0.201	-0.0841	0.4057	-0.1091	-0.1724	1.0213	0.0817	0.0949	0.5873	0.0589	0.894	-102.8507	-60.8743	-39.2018
3	0.7131	-0.3034	-0.8763	1.3067	0.6669	4.1091	0.0856	-0.1442	0.0917	-0.0518	0.1948	-0.4321	0.1288	0.5216	-0.342	0.7053	0.0643	0.0045	0.6566	-0.0763	0.9646	-84.7238	-45.3394	-41.1692
4	0.7517	-0.3377	-0.6775	0.744	0.7103	4.737	0.167	-0.0867	0.2459	-0.0199	0.2008	-0.282	-0.254	0.0786	-0.3029	1.0988	0.017	0.2496	0.6235	-0.0561	0.9961	-93.8521	-23.8392	-46.7716
5	0.3573	0.0864	0.1474	1.463	0.8675	6.0775	0.1277	-0.1184	0.1635	0.0207	0.0381	0.1209	-0.6197	-0.7338	-0.1197	0.9123	0.2762	0.1531	0.9058	0.1253	0.8152	-117.8325	-26.2308	-48.4799
6	3.9581	1.1302	-0.2355	1.4545	0.0439	0.6459	-0.0487	-0.6898	-0.1659	0.3144	-0.0747	-0.2613	0.1219	0.0029	0.1413	0.9015	0.1179	0.1211	0.8741	0.1687	1.0653	-80.5598	-118.1956	-17.492
7	3.8091	0.8668	0.2691	1.1479	-0.0467	0.859	-0.2887	-0.1312	-0.3081	-0.2317	0.0526	-0.2099	0.2302	0.2294	0.1983	1.0007	0.0667	0.2573	0.6441	0.0827	1.0339	-76.7891	-128.2565	-38.968
8	6.2403	0.7614	1.8816	1.3117	-0.1048	1.3348	-0.1071	0.7306	-0.0464	-0.2965	0.0257	-0.2226	0.1936	0.3494	0.2641	1.0905	-0.0378	0.2169	0.6592	-0.0048	0.9137	-79.3463	-111.301	-55.703
9	4.9964	0.4904	0.4981	1.1071	-0.1953	0.6699	-0.2734	0.0887	0.096	-0.0825	0.0953	-0.306	-0.1436	0.1009	0.2951	0.9778	0.0347	0.0851	0.6587	0.0523	1.2065	-84.6411	-90.6236	-44.7122
10	5.5819	0.4678	-0.2233	0.8351	-0.5493	0.6087	-0.2096	-0.6333	0.3445	0.3049	0.0398	-0.0338	-0.1008	0.0805	0.1941	0.8895	0.0966	0.052	0.848	-0.2201	0.9763	-85.4133	-94.9498	-20.9881

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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