PDB-2xxr: Crystal structure of the GluK2 (GluR6) wild-type LBD dimer in com...

ID or keywords:

Entry

Database: PDB / ID: 2xxr

Title

Crystal structure of the GluK2 (GluR6) wild-type LBD dimer in complex with glutamate

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 / negative regulation of synaptic transmission, glutamatergic / regulation of short-term neuronal synaptic plasticity / inhibitory postsynaptic potential / glutamate receptor activity / ubiquitin conjugating enzyme binding ...
Similarity search - Function

Biological species

RATTUS NORVEGICUS (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 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 11, 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 / 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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	2xxr.cif.gz	221.9 KB	Display	PDBx/mmCIF format
PDB format	pdb2xxr.ent.gz	178.5 KB	Display	PDB format
PDBx/mmJSON format	2xxr.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2xxr_validation.pdf.gz	449.1 KB	Display	wwPDB validaton report
Full document	2xxr_full_validation.pdf.gz	452.5 KB	Display
Data in XML	2xxr_validation.xml.gz	24.5 KB	Display
Data in CIF	2xxr_validation.cif.gz	36.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xx/2xxr ftp://data.pdbj.org/pub/pdb/validation_reports/xx/2xxr	HTTPS FTP

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Related structure data

Related structure data	2xxtC 2xxuC 2xxvC 2xxwC 2xxxC 2xxyC 1s50S 1s7y 1s9t 1sd3 1tt1 1yae 2i0b 2i0c C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4bdq-d 2xxv-d 2xxw-d 2xxy-2 2xxu-d 1m5f-2 3kei-1 2xxt-d 1my0-2 1my1-1 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

hetero molecules

59.6 kDa, 2 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)	95.326, 105.464, 114.278
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

#1: Protein	GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 2 / GLUTAMATE RECEPTOR 6 / GLUR-6 / GLUR6 Mass: 29625.943 Da / Num. of mol.: 2 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 429-544,667-806 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.: 2 / Source method: obtained synthetically / Formula: C₅H₉NO₄
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 50 % / Description: NONE
Crystal grow	Method: vapor diffusion, hanging drop Details: VAPOR DIFFUSION, HANGING DROP. 27% PEG 4000, 3% 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: 1.6→19.4 Å / Num. obs: 75578 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / B_iso Wilson estimate: 20.44 Å² / R_merge(I) obs: 0.05 / Net I/σ(I): 18.9
Reflection shell	Resolution: 1.6→1.64 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.66 / Mean I/σ(I) obs: 2.3 / % 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 1S50

1s50

Resolution: 1.6→19.439 Å / SU ML: 0.21 / σ(F): 1.99 / Phase error: 18.24 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1948	3780	5 %
R_work	0.1693	-	-
obs	0.1706	75578	99.56 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 60.249 Å² / k_sol: 0.4 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.8358 Å²	0 Å²	0 Å²
2-	-	0.6108 Å²	-0 Å²
3-	-	-	0.225 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→19.439 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3975	0	23	477	4475

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4108
X-RAY DIFFRACTION	f_angle_d	1.016	5535
X-RAY DIFFRACTION	f_dihedral_angle_d	15.408	1529
X-RAY DIFFRACTION	f_chiral_restr	0.072	619
X-RAY DIFFRACTION	f_plane_restr	0.004	696

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 (%)
1.6-1.6203	0.2831	139	0.2395	2625	X-RAY DIFFRACTION	100
1.6203-1.6416	0.2786	137	0.2257	2605	X-RAY DIFFRACTION	100
1.6416-1.6641	0.2419	139	0.225	2649	X-RAY DIFFRACTION	100
1.6641-1.6878	0.2641	140	0.2131	2665	X-RAY DIFFRACTION	100
1.6878-1.713	0.2326	139	0.204	2630	X-RAY DIFFRACTION	100
1.713-1.7397	0.2345	138	0.1936	2617	X-RAY DIFFRACTION	100
1.7397-1.7682	0.215	140	0.183	2663	X-RAY DIFFRACTION	99
1.7682-1.7987	0.2039	138	0.1827	2623	X-RAY DIFFRACTION	100
1.7987-1.8314	0.2079	139	0.1701	2645	X-RAY DIFFRACTION	100
1.8314-1.8666	0.2172	140	0.179	2658	X-RAY DIFFRACTION	100
1.8666-1.9047	0.2271	140	0.1739	2662	X-RAY DIFFRACTION	100
1.9047-1.946	0.1984	138	0.1725	2630	X-RAY DIFFRACTION	100
1.946-1.9913	0.201	140	0.1652	2649	X-RAY DIFFRACTION	100
1.9913-2.041	0.2042	139	0.1591	2649	X-RAY DIFFRACTION	100
2.041-2.0961	0.1899	139	0.15	2630	X-RAY DIFFRACTION	100
2.0961-2.1577	0.1807	142	0.1501	2694	X-RAY DIFFRACTION	100
2.1577-2.2273	0.1777	140	0.1554	2674	X-RAY DIFFRACTION	100
2.2273-2.3068	0.176	138	0.1541	2622	X-RAY DIFFRACTION	100
2.3068-2.399	0.2061	142	0.157	2697	X-RAY DIFFRACTION	100
2.399-2.5079	0.1801	141	0.1649	2677	X-RAY DIFFRACTION	100
2.5079-2.6399	0.1988	140	0.1646	2653	X-RAY DIFFRACTION	100
2.6399-2.8048	0.1645	141	0.1751	2686	X-RAY DIFFRACTION	100
2.8048-3.0206	0.2023	142	0.1715	2691	X-RAY DIFFRACTION	100
3.0206-3.3233	0.2079	141	0.1711	2676	X-RAY DIFFRACTION	100
3.3233-3.801	0.1816	142	0.1592	2713	X-RAY DIFFRACTION	99
3.801-4.7771	0.1447	142	0.1376	2687	X-RAY DIFFRACTION	98
4.7771-19.4401	0.1798	144	0.1684	2728	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	1.1396	0.9392	0.1599	1.2672	0.236	1.1309	-0.1058	0.076	-0.1867	-0.001	0.0429	-0.0288	0.2036	-0.133	0.0507	0.1406	-0.0374	0.0417	0.1355	0.014	0.1765	-40.974	24.5223	13.9299
2	1.1706	0.2111	-0.9965	1.5799	-0.0389	1.7535	-0.0437	0.0424	-0.0105	-0.1743	0.0611	-0.0632	0.0286	-0.0257	-0.0141	0.1024	-0.023	0.0024	0.086	0.0208	0.0929	-28.8365	38.5109	5.866
3	1.9939	-0.188	-0.6249	2.0778	0.8408	1.5708	-0.0106	0.1956	-0.2276	-0.3361	-0.0384	-0.1174	0.0092	-0.0454	0.0458	0.1318	0.0126	0.0263	0.1319	-0.0029	0.124	-18.5595	33.2905	1.61
4	0.9739	1.107	0.4151	1.4241	0.2887	0.4159	0.0691	-0.0685	0.0106	0.1336	-0.1492	0.019	0.0208	-0.0477	0.0671	0.1304	-0.0063	0.0344	0.1473	0.025	0.1304	-34.7099	34.4833	22.3501
5	5.5232	-4.1127	-4.5417	3.0739	3.4212	3.8709	-0.3079	0.107	-0.1532	-0.208	-0.1352	0.1382	-0.1058	0.005	0.3156	0.1465	0.0091	0.011	0.2302	-0.0365	0.224	-27.7272	35.4119	5.9872
6	1.232	1.0891	0.0928	1.6095	0.651	0.4973	-0.062	-0.0769	0.1426	-0.1076	0.0458	-0.0752	-0.1067	0.0188	0.0164	0.1683	0.0263	-0.0171	0.1245	-0.022	0.1603	-18.9283	62.8612	26.6553
7	1.4413	-0.1367	0.3968	0.8915	-0.5591	0.9943	0.0162	-0.2422	-0.0041	0.1531	-0.0087	0.0913	0.0175	-0.133	-0.0041	0.1655	0.0061	0.0226	0.1702	-0.0139	0.1052	-25.9593	46.1711	35.6238
8	2.043	-0.7457	1.0269	1.7323	-0.1915	1.7602	-0.1118	-0.3327	0.0621	0.2379	0.044	-0.1147	0.0166	-0.1202	0.0502	0.1827	0.0309	-0.0229	0.1745	0.0115	0.1434	-16.7281	39.9619	40.895
9	1.1386	0.8481	0.5722	1.9373	0.4594	0.8194	-0.0879	0.1148	-0.0256	-0.1401	0.0695	-0.0383	-0.0312	0.0393	0.0152	0.1422	0.0134	0.0014	0.1331	0.0178	0.1229	-23.3804	52.2683	18.7376
10	2.3367	2.1687	2.2086	2.0127	2.0498	2.0876	-0.0462	-0.3544	-0.294	0.1503	0.1722	0.1809	-0.0283	-0.3185	-0.1438	0.2254	0.0709	-0.0222	0.1957	0.0174	0.1876	-22.7868	46.5518	35.531

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(CHAIN A AND RESID 429:483)
2	X-RAY DIFFRACTION	2	(CHAIN A AND RESID 484:677)
3	X-RAY DIFFRACTION	3	(CHAIN A AND RESID 678:762)
4	X-RAY DIFFRACTION	4	(CHAIN A AND RESID 763:805)
5	X-RAY DIFFRACTION	5	(CHAIN A AND RESID 900)
6	X-RAY DIFFRACTION	6	(CHAIN B AND RESID 429:483)
7	X-RAY DIFFRACTION	7	(CHAIN B AND RESID 484:677)
8	X-RAY DIFFRACTION	8	(CHAIN B AND RESID 678:762)
9	X-RAY DIFFRACTION	9	(CHAIN B AND RESID 763:805)
10	X-RAY DIFFRACTION	10	(CHAIN B AND RESID 900)

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