PDB-3zkr: X-ray structure of a pentameric ligand gated ion channel from Erw...

ID or keywords:

Entry

Database: PDB / ID: 3zkr

Title

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

Components

CYS-LOOP LIGAND-GATED ION CHANNEL

Keywords

TRANSPORT PROTEIN / CYS-LOOP RECEPTOR / GABA-A RECEPTOR / GENERAL ANESTHETICS

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

ERWINIA CHRYSANTHEMI (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.649 Å

Authors

Spurny, R. / Billen, B. / Howard, R.J. / Brams, M. / Debaveye, S. / Price, K.L. / Weston, D.A. / Strelkov, S.V. / Tytgat, J. / Bertrand, S. ...

Citation

Journal: J.Biol.Chem. / Year: 2013
Title: Multisite Binding of a General Anesthetic to the Prokaryotic Pentameric Erwinia Chrysanthemi Ligand-Gated Ion Channel (Elic).
Authors: Spurny, R. / Billen, B. / Howard, R.J. / Brams, M. / Debaveye, S. / Price, K.L. / Weston, D.A. / Strelkov, S.V. / Tytgat, J. / Bertrand, S. / Bertrand, D. / Lummis, S.C.R. / Ulens, C.

History

Deposition	Jan 24, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2013	Group: Database references
Revision 1.2	Sep 17, 2014	Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other
Revision 1.3	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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	3zkr.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb3zkr.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	3zkr.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3zkr_validation.pdf.gz	3.2 MB	Display	wwPDB validaton report
Full document	3zkr_full_validation.pdf.gz	3.3 MB	Display
Data in XML	3zkr_validation.xml.gz	107.4 KB	Display
Data in CIF	3zkr_validation.cif.gz	141.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zk/3zkr ftp://data.pdbj.org/pub/pdb/validation_reports/zk/3zkr	HTTPS FTP

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Related structure data

Similar structure data	4twd-1 4twf-1 3uq7-1 2vl0-1 3uq4-1 4a98-2 4a97-1 3uq5-2 4a97-2 6v0b-d 4twh-2 3rqu-2 2yoe-2 4a98-1 5heo-2 3uq4-2 5heu-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

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

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

1

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

2

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

Unit cell

Length a, b, c (Å)	105.109, 266.248, 110.746
Angle α, β, γ (deg.)	90.00, 109.78, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1
5	1
6	1
7	1
8	1
9	1
10	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A AND (RESSEQ 11:177 OR RESSEQ 184: 317 )
2	1	1	CHAIN B AND (RESSEQ 11:177 OR RESSEQ 184: 317 )
3	1	1	CHAIN C AND (RESSEQ 11:177 OR RESSEQ 184: 317 )
4	1	1	CHAIN D AND (RESSEQ 11:177 OR RESSEQ 184: 317 )
5	1	1	CHAIN E AND (RESSEQ 11:177 OR RESSEQ 184: 317 )
6	1	1	CHAIN F AND (RESSEQ 11:177 OR RESSEQ 184: 317 )
7	1	1	CHAIN G AND (RESSEQ 11:177 OR RESSEQ 184: 317 )
8	1	1	CHAIN H AND (RESSEQ 11:177 OR RESSEQ 184: 317 )
9	1	1	CHAIN I AND (RESSEQ 11:177 OR RESSEQ 184: 317 )
10	1	1	CHAIN J AND (RESSEQ 11:177 OR RESSEQ 184: 317 )

#1: Protein	CYS-LOOP LIGAND-GATED ION CHANNEL / ELIC Mass: 35383.367 Da / Num. of mol.: 10 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-MBR / TRIBROMOMETHANE Mass: 252.731 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: CHBr₃

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 4.12 Å³/Da / Density % sol: 70.15 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9193
Detector	Date: Sep 10, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9193 Å / Relative weight: 1
Reflection	Resolution: 3.65→44.08 Å / Num. obs: 62852 / % possible obs: 98.9 % / Observed criterion σ(I): 2.1 / Redundancy: 3.8 % / B_iso Wilson estimate: 105.99 Å² / R_merge(I) obs: 0.11 / Net I/σ(I): 9.5

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Processing

Software

Name: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.649→44.083 Å / SU ML: 0.4 / σ(F): 1.34 / Phase error: 28.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2639	3185	5.1 %
R_work	0.2287	-	-
obs	0.2305	62779	98.88 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.649→44.083 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25020	0	22	0	25042

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	25700
X-RAY DIFFRACTION	f_angle_d	1.335	35030
X-RAY DIFFRACTION	f_dihedral_angle_d	16.725	9210
X-RAY DIFFRACTION	f_chiral_restr	0.102	3890
X-RAY DIFFRACTION	f_plane_restr	0.009	4470

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	2459	X-RAY DIFFRACTION	POSITIONAL
1	2	B	2459	X-RAY DIFFRACTION	POSITIONAL	0.092
1	3	C	2459	X-RAY DIFFRACTION	POSITIONAL	0.109
1	4	D	2459	X-RAY DIFFRACTION	POSITIONAL	0.097
1	5	E	2459	X-RAY DIFFRACTION	POSITIONAL	0.108
1	6	F	2459	X-RAY DIFFRACTION	POSITIONAL	0.1
1	7	G	2459	X-RAY DIFFRACTION	POSITIONAL	0.089
1	8	H	2459	X-RAY DIFFRACTION	POSITIONAL	0.095
1	9	I	2459	X-RAY DIFFRACTION	POSITIONAL	0.137
1	10	J	2459	X-RAY DIFFRACTION	POSITIONAL	0.084

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 (%)
3.6485-3.703	0.3339	123	0.3321	2345	X-RAY DIFFRACTION	90
3.703-3.7608	0.3488	131	0.3144	2658	X-RAY DIFFRACTION	100
3.7608-3.8224	0.3105	119	0.285	2601	X-RAY DIFFRACTION	100
3.8224-3.8883	0.3048	164	0.2783	2590	X-RAY DIFFRACTION	100
3.8883-3.9589	0.3053	124	0.266	2600	X-RAY DIFFRACTION	100
3.9589-4.035	0.2914	144	0.255	2642	X-RAY DIFFRACTION	100
4.035-4.1173	0.3024	146	0.2538	2587	X-RAY DIFFRACTION	100
4.1173-4.2068	0.2658	162	0.238	2603	X-RAY DIFFRACTION	100
4.2068-4.3046	0.2738	138	0.2265	2606	X-RAY DIFFRACTION	100
4.3046-4.4121	0.2677	129	0.2202	2620	X-RAY DIFFRACTION	100
4.4121-4.5313	0.2165	136	0.2066	2584	X-RAY DIFFRACTION	100
4.5313-4.6645	0.2298	138	0.1939	2610	X-RAY DIFFRACTION	100
4.6645-4.8149	0.2479	124	0.1913	2637	X-RAY DIFFRACTION	100
4.8149-4.9868	0.2159	136	0.205	2625	X-RAY DIFFRACTION	99
4.9868-5.1861	0.2162	124	0.1943	2603	X-RAY DIFFRACTION	100
5.1861-5.4218	0.2755	138	0.2017	2602	X-RAY DIFFRACTION	100
5.4218-5.707	0.2457	133	0.2151	2610	X-RAY DIFFRACTION	100
5.707-6.0638	0.267	156	0.2103	2612	X-RAY DIFFRACTION	99
6.0638-6.5306	0.2439	136	0.2236	2642	X-RAY DIFFRACTION	99
6.5306-7.1852	0.2683	150	0.2344	2543	X-RAY DIFFRACTION	99
7.1852-8.2191	0.2497	145	0.2232	2588	X-RAY DIFFRACTION	98
8.2191-10.3332	0.1891	154	0.1863	2522	X-RAY DIFFRACTION	96
10.3332-44.0864	0.3258	135	0.2617	2564	X-RAY DIFFRACTION	96

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	0.49	0.0808	0.5638	2.6677	1.9136	7.6993	0.1411	-0.2139	-0.3225	0.5826	-0.1046	0.7601	0.4779	-1.1393	0.1414	0.8702	-0.1491	0.2489	0.9021	0.0591	0.8315	-122.8466	-50.2161	-44.4561
2	1.1894	0.413	-0.1125	2.3206	0.8192	6.8741	0.2467	-0.2299	0.0496	0.1839	0.0769	-0.136	0.0175	-0.0898	-0.2526	0.8638	0.0623	0.036	0.3807	0.0214	0.7266	-102.4159	-62.2945	-39.7263
3	1.2735	-0.0732	-0.8998	2.1118	1.178	7.0886	0.1414	-0.2126	0.1029	0.2696	0.2122	-0.7125	0.5211	0.7671	-0.4427	0.6329	0.0784	-0.0284	0.3993	-0.0822	0.6929	-83.9134	-47.0041	-41.3016
4	1.4997	-0.3015	-0.8074	1.2527	1.2535	2.9672	0.2118	-0.0875	0.3717	0.1113	0.1922	-0.2073	0.0789	0.23	-0.1332	1.0355	0.0383	0.338	0.5525	-0.1147	0.9466	-92.681	-25.2144	-46.7826
5	0.7907	0.3492	-0.5389	2.7739	0.0384	4.4464	0.2077	-0.0641	0.1367	-0.1415	0.1883	0.4194	-1.2399	-0.5277	-0.1402	0.802	0.2721	0.195	0.7646	0.1464	0.7079	-116.8479	-27.1866	-48.8097
6	8.8617	1.6049	-0.2205	2.083	0.3684	1.1167	0.006	-0.8986	0.4064	0.6922	-0.0299	-0.1002	0.1413	0.0016	-0.0445	0.9732	0.2197	0.1169	0.6729	0.168	0.8518	-79.8978	-118.969	-17.3251
7	7.2206	2.5613	0.1496	1.6587	0.1081	1.2337	-0.3929	-0.2042	-0.6607	-0.1936	0.1645	-0.2296	0.2194	0.2885	0.1688	0.7259	0.1353	0.2498	0.4431	0.0635	1.0491	-76.3057	-129.4223	-38.8866
8	7.9735	0.5344	1.658	2.2496	0.1235	1.0241	-0.0757	0.6638	-0.2336	-0.3699	0.0664	-0.409	0.0441	0.2452	0.0822	0.8125	-0.0892	0.1612	0.5112	0.0382	0.6919	-78.9746	-112.7037	-56.1398
9	8.8419	1.9785	0.0345	1.1986	-0.0328	1.309	-0.4874	-0.061	-0.16	-0.0712	0.1845	-0.5911	-0.2186	0.1594	0.3885	0.6834	0.0424	0.0129	0.3404	0.0852	1.4168	-84.2366	-91.7701	-45.3306
10	8.0424	1.5148	-0.6338	1.5939	-0.5642	1.0206	-0.2634	-0.9121	0.4112	0.5158	0.0772	-0.0523	-0.1437	0.0261	0.1783	0.8388	0.2767	-0.0439	0.6745	-0.2323	0.9018	-84.8477	-95.6232	-21.3933

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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