PDB-2xxx: Crystal structure of the GluK2 (GluR6) D776K LBD dimer in complex...

ID or keywords:

Entry

Database: PDB / ID: 2xxx

Title

Crystal structure of the GluK2 (GluR6) D776K LBD dimer in complex with glutamate (P21 21 21)

Components

GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2

Keywords

TRANSPORT PROTEIN

Function / homology

Function and homology information

mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / kainate selective glutamate receptor complex / Activation of Ca-permeable Kainate Receptor / regulation of short-term neuronal synaptic plasticity / glutamate receptor activity / negative regulation of synaptic transmission, glutamatergic / ubiquitin conjugating enzyme binding / regulation of JNK cascade ...
Similarity search - Function

Biological species

RATTUS NORVEGICUS (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.098 Å

Authors

Nayeem, N. / Mayans, O. / Green, T.

Citation

Journal: J.Neurosci. / Year: 2011
Title: Conformational Flexibility of the Ligand-Binding Domain Dimer in Kainate Receptor Gating and Desensitization
Authors: Nayeem, N. / Mayans, O. / Green, T.

History

Deposition	Nov 12, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 9, 2011	Provider: repository / Type: Initial release
Revision 1.1	Apr 4, 2012	Group: Database references / Refinement description / Version format compliance
Revision 1.2	Jan 30, 2019	Group: Data collection / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3	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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Download

PDBx/mmCIF format	2xxx.cif.gz	415.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2xxx.ent.gz	341.8 KB	Display	PDB format
PDBx/mmJSON format	2xxx.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2xxx_validation.pdf.gz	472.8 KB	Display	wwPDB validaton report
Full document	2xxx_full_validation.pdf.gz	483.3 KB	Display
Data in XML	2xxx_validation.xml.gz	40.2 KB	Display
Data in CIF	2xxx_validation.cif.gz	56.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xx/2xxx ftp://data.pdbj.org/pub/pdb/validation_reports/xx/2xxx	HTTPS FTP

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Related structure data

Related structure data	2xxrSC 2xxtC 2xxuC 2xxvC 2xxwC 2xxyC 1s50 1s7y 1s9t 1sd3 1tt1 1yae 2i0b 2i0c S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4bdl-d 4bdn-1 4bdm-2 2xxy-1 3g3h-d 4bdm-1 3g3i-d 3fvk-d 4e0x-d 3g3g-d 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	#235 - Jul 2019 AMPA Receptor similarity (13) #199 - Jul 2016 Monellin similarity (2) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1)

Deposited unit

A: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2

B: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2

C: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2

D: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2

hetero molecules

119 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2

B: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2

hetero molecules

defined by author&software
59.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2

D: GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2

hetero molecules

defined by author&software
59.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.560, 101.341, 125.697
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2 / GLUTAMATE RECEPTOR 6 / GLUR-6 / GLUR6 Mass: 29640.037 Da / Num. of mol.: 4 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 429-544,667-806 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42260
#2: Chemical	ChemComp-GLU / GLUTAMIC ACID Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₉NO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 394 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, ASP 776 TO LYS ENGINEERED RESIDUE IN CHAIN B, ASP 776 TO LYS ...ENGINEERED RESIDUE IN CHAIN A, ASP 776 TO LYS ENGINEERED RESIDUE IN CHAIN B, ASP 776 TO LYS ENGINEERED RESIDUE IN CHAIN C, ASP 776 TO LYS ENGINEERED RESIDUE IN CHAIN D, ASP 776 TO LYS

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47 % / Description: NONE
Crystal grow	Method: vapor diffusion, hanging drop Details: VAPOR DIFFUSION, HANGING DROP 21% PEG 4000, 9% PROPAN-2-OL, 80MM SODIUM ACETATE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97
Detector	Type: ADSC CCD / Detector: CCD
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.1→19.9 Å / Num. obs: 63552 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / B_iso Wilson estimate: 32.4 Å² / R_merge(I) obs: 0.06 / Net I/σ(I): 15.6
Reflection shell	Resolution: 2.1→2.15 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.65 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XXR

2xxr

Resolution: 2.098→19.928 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 22.58 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2309	3232	5.1 %
R_work	0.1786	-	-
obs	0.1812	63552	98.52 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 43.155 Å² / k_sol: 0.329 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.0963 Å²	0 Å²	0 Å²
2-	-	4.4804 Å²	0 Å²
3-	-	-	-0.3841 Å²

Refinement step

Cycle: LAST / Resolution: 2.098→19.928 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7920	0	40	394	8354

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	8107
X-RAY DIFFRACTION	f_angle_d	0.816	10919
X-RAY DIFFRACTION	f_dihedral_angle_d	15.75	3005
X-RAY DIFFRACTION	f_chiral_restr	0.059	1217
X-RAY DIFFRACTION	f_plane_restr	0.003	1368

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 (%)
2.0981-2.1294	0.3321	138	0.2481	2420	X-RAY DIFFRACTION	93
2.1294-2.1626	0.3141	147	0.2525	2615	X-RAY DIFFRACTION	100
2.1626-2.198	0.2872	146	0.2353	2634	X-RAY DIFFRACTION	100
2.198-2.2359	0.2941	138	0.2316	2595	X-RAY DIFFRACTION	100
2.2359-2.2765	0.2848	118	0.2172	2652	X-RAY DIFFRACTION	100
2.2765-2.3202	0.2551	148	0.2059	2617	X-RAY DIFFRACTION	99
2.3202-2.3675	0.2674	148	0.2082	2635	X-RAY DIFFRACTION	99
2.3675-2.4189	0.2837	144	0.1989	2594	X-RAY DIFFRACTION	99
2.4189-2.475	0.2622	153	0.2059	2612	X-RAY DIFFRACTION	100
2.475-2.5368	0.27	146	0.1837	2632	X-RAY DIFFRACTION	99
2.5368-2.6053	0.2107	138	0.1842	2632	X-RAY DIFFRACTION	99
2.6053-2.6818	0.2263	139	0.1778	2632	X-RAY DIFFRACTION	99
2.6818-2.7681	0.2553	139	0.1919	2629	X-RAY DIFFRACTION	99
2.7681-2.8668	0.279	138	0.1978	2609	X-RAY DIFFRACTION	99
2.8668-2.9812	0.2267	140	0.1927	2635	X-RAY DIFFRACTION	99
2.9812-3.1164	0.2215	140	0.1909	2620	X-RAY DIFFRACTION	99
3.1164-3.28	0.2584	138	0.1889	2632	X-RAY DIFFRACTION	99
3.28-3.4845	0.2279	140	0.1752	2648	X-RAY DIFFRACTION	99
3.4845-3.7519	0.2056	139	0.1665	2633	X-RAY DIFFRACTION	98
3.7519-4.1264	0.1972	139	0.1482	2651	X-RAY DIFFRACTION	98
4.1264-4.7166	0.1808	137	0.1322	2635	X-RAY DIFFRACTION	97
4.7166-5.9165	0.2018	139	0.1449	2645	X-RAY DIFFRACTION	96
5.9165-19.9285	0.1797	140	0.1563	2713	X-RAY DIFFRACTION	95

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	2.3938	-0.0449	0.0689	0.6783	-0.1732	2.49	0.0677	0.3987	0.1313	-0.2103	-0.0733	0.18	-0.5724	-0.3836	0.0036	0.2628	0.0811	-0.0249	0.2345	-0.0023	0.2476	-26.4447	9.0474	-23.7482
2	1.0581	-0.8003	-0.7536	2.2584	-1.3729	3.5037	0.1718	-0.1479	0.3217	-0.0597	-0.2164	-0.2684	-0.183	0.7449	0.0438	0.1772	-0.0921	0.0307	0.3141	-0.0322	0.2427	-8.6514	10.0352	-19.4712
3	2.4177	-0.876	-0.108	1.5052	-0.0237	3.4239	0.1292	0.5057	-0.049	-0.2214	-0.1895	-0.4871	0.6061	1.4108	0.0396	0.31	0.2077	0.0594	0.7134	-0.013	0.2316	-0.0924	-8.8378	-28.8003
4	2.3373	-0.6804	0.3702	2.8052	0.6252	4.4275	0.2024	0.4929	-0.0986	-0.4728	-0.3075	0.284	0.3384	0.8093	0.0326	0.2286	0.1359	-0.0301	0.3181	-0.0165	0.0725	-11.2683	-6.4276	-29.4127
5	0.9947	-0.6686	-0.5209	0.7791	-0.3463	1.8457	-0.0847	-0.2921	-0.1012	0.2151	0.0638	0.252	0.1513	0.1329	0.0169	0.1201	0.0201	0.005	0.1421	-0.0523	0.1614	-22.9891	2.0285	-10.8652
6	1.9025	-0.3952	-0.7121	2.5003	0.0636	1.6779	-0.0955	-0.8744	0.0612	0.4558	0.1691	-0.1821	0.049	1.0426	-0.0473	0.2352	0.1135	-0.0597	0.8374	-0.0843	0.1295	-6.2094	-3.189	8.7684
7	1.8864	-1.786	-0.25	1.8225	0.7018	1.6582	0.0327	0.2657	-0.6894	0.0374	0.118	0.8355	0.8262	0.2511	-0.1602	0.4661	0.1536	-0.0749	0.1419	0.0171	0.3803	-24.0411	-23.0874	-1.0937
8	1.9337	0.1686	-1.2393	2.0192	0.332	2.3802	0.0192	-0.4602	-0.2151	0.455	0.2087	0.2675	0.3147	0.0423	-0.1448	0.3209	0.1146	0.0543	0.222	0.1131	0.2084	-27.6668	-14.6867	8.0861
9	1.0088	0.2285	-0.5024	1.0101	0.2254	1.985	-0.0935	-0.0661	-0.0949	0.1077	0.3127	-0.2119	0.4567	0.8908	-0.0878	0.2901	0.227	-0.0233	0.3499	0.02	0.1576	-14.9936	-14.8254	2.2431
10	0.4549	-0.4941	0.3438	0.798	-1.1777	2.6853	0.1815	0.0565	0.2843	-0.2536	-0.3636	-0.1184	0.1366	1.3059	0.1672	0.1777	0.11	-0.0258	0.7141	-0.0212	0.2332	-0.7618	-6.373	-6.4907
11	0.3175	-0.1495	0.6002	1.2837	0.8572	2.2075	-0.013	-0.4213	0.1459	0.5316	-0.3772	0.5634	0.3942	-1.541	0.3396	0.2863	-0.1141	0.2619	0.9061	-0.1559	0.3492	-66.4	7.4812	12.8767
12	1.3315	-0.1017	0.0608	1.9524	0.9849	2.4573	-0.1022	-0.4917	-0.0951	0.4964	-0.0096	0.0912	0.5111	-0.2976	0.1189	0.2958	0.0329	0.0632	0.3606	0.0448	0.1456	-48.7951	4.5593	8.3946
13	2.6019	-0.1342	1.7169	2.5175	1.1337	2.5164	-0.0656	-0.323	0.065	0.2867	0.2331	-0.268	-0.0555	0.1683	-0.1429	0.2302	0.0876	-0.0156	0.2332	-0.0451	0.1842	-36.9294	16.5213	7.1632
14	0.9999	0.0068	-0.7712	0.9638	0.2498	0.6568	-0.1752	-0.0386	0.1087	-0.1511	0.0577	0.1625	-0.2381	-0.413	0.1016	0.2943	0.1941	-0.0052	0.2015	-0.0573	0.1612	-48.4364	21.866	3.5695
15	0.0732	0.1602	-0.1977	2.0964	0.5474	2.7582	-0.1107	0.0373	0.016	0.2374	-0.1733	0.7049	0.2455	-1.1661	0.2472	0.2031	-0.0593	0.1006	0.5775	-0.0537	0.3595	-62.9174	3.0956	-0.5818
16	2.2348	0.3645	-1.023	1.031	0.4412	2.5345	0.0135	0.3604	-0.0537	-0.0251	0.0832	0.008	0.7278	0.115	-0.0728	0.2721	0.0495	0.0156	0.1227	-0.0139	0.2088	-41.1885	-8.4707	-22.6486
17	2.6235	-0.0782	0.2147	2.6575	1.1916	3.8377	-0.0075	0.0677	-0.346	0.1178	-0.1912	0.4331	0.6893	-0.7009	0.2034	0.2719	-0.152	0.0417	0.2381	0.0108	0.3584	-57.531	-9.0891	-16.4639
18	4.3032	0.4744	1.3805	1.3258	-0.3374	2.6725	0.1787	0.8562	0.4187	-0.1702	-0.0001	0.2029	0.0182	-0.3336	-0.1693	0.1176	0.038	-0.0001	0.4672	0.1427	0.27	-65.4311	8.1361	-27.2555
19	2.7868	-1.1701	0.8963	0.4838	-0.491	1.7217	-0.0129	0.3335	0.5034	0.0209	-0.2527	-0.3088	0.1548	-0.1085	0.2778	0.1694	-0.0231	0.0838	0.1859	0.0756	0.3156	-53.0109	4.4378	-18.6903
20	1.8858	-0.2886	-1.0626	0.5118	0.835	1.5582	-0.0866	-0.1563	0.3943	0.2144	0.226	0.0174	-0.1631	0.0022	-0.1206	0.1404	0.0377	0.0092	0.1125	0.0315	0.206	-41.6184	1.7233	-10.4396

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 432:483)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 484:535)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 536:712)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 713:769)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 770:799)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 432:534)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 535:673)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 674:726)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 727:775)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 776:799)
11	X-RAY DIFFRACTION	11	(CHAIN C AND RESID 432:482)
12	X-RAY DIFFRACTION	12	(CHAIN C AND RESID 483:668)
13	X-RAY DIFFRACTION	13	(CHAIN C AND RESID 669:726)
14	X-RAY DIFFRACTION	14	(CHAIN C AND RESID 727:763)
15	X-RAY DIFFRACTION	15	(CHAIN C AND RESID 764:799)
16	X-RAY DIFFRACTION	16	(CHAIN D AND RESID 431:483)
17	X-RAY DIFFRACTION	17	(CHAIN D AND RESID 484:535)
18	X-RAY DIFFRACTION	18	(CHAIN D AND RESID 536:741)
19	X-RAY DIFFRACTION	19	(CHAIN D AND RESID 742:775)
20	X-RAY DIFFRACTION	20	(CHAIN D AND RESID 776:799)

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Yorodumi