PDB-2qs4: Crystal structure of the GluR5 ligand binding core dimer in compl...

ID or keywords:

Entry

Database: PDB / ID: 2qs4

Title

Crystal structure of the GluR5 ligand binding core dimer in complex with LY466195 at 1.58 Angstroms resolution

Components

Glutamate receptor, ionotropic kainate 1

Keywords

MEMBRANE PROTEIN /

Cell junction /

Glycoprotein /

Ion transport /

Ionic channel /

Phosphorylation / Postsynaptic cell membrane / Receptor /

RNA editing /

Synapse /

Transmembrane / Transport

Function / homology

Function and homology information

gamma-aminobutyric acid secretion / negative regulation of synaptic transmission, GABAergic / L-glutamate transmembrane transporter activity / positive regulation of gamma-aminobutyric acid secretion / 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 ...
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.58 Å

Authors

Alushin, G.M. / Jane, D.E. / Mayer, M.L.

Citation

Journal: Neuropharmacology / Year: 2011
Title: Binding site and ligand flexibility revealed by high resolution crystal structures of GluK1 competitive antagonists.
Authors: Alushin, G.M. / Jane, D. / Mayer, M.L.

History

Deposition	Jul 30, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 5, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 22, 2012	Group: Database references
Revision 1.3	Aug 5, 2015	Group: Non-polymer description
Revision 1.4	Aug 2, 2017	Group: Source and taxonomy / Category: entity_src_gen
Revision 1.5	Oct 20, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6	Aug 30, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2qs4.cif.gz	250.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2qs4.ent.gz	204.1 KB	Display	PDB format
PDBx/mmJSON format	2qs4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qs/2qs4 ftp://data.pdbj.org/pub/pdb/validation_reports/qs/2qs4	HTTPS FTP

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Related structure data

Related structure data	2qs1C 2qs2C 2f34S 1txf 2f35 2f36 2qs3 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4ovz-d 5nec-2 6fbe-d 1qss-d 5szt-d 2v3t-d 3pzp-2 5ytg-d 1qtm-d 6iml-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 (11) #199 - Jul 2016 Monellin similarity (2) #135 - Mar 2011 Integrase similarity (1)

Deposited unit

A: Glutamate receptor, ionotropic kainate 1

B: Glutamate receptor, ionotropic kainate 1

C: Glutamate receptor, ionotropic kainate 1

D: Glutamate receptor, ionotropic kainate 1

hetero molecules

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

1

A: Glutamate receptor, ionotropic kainate 1

C: Glutamate receptor, ionotropic kainate 1

hetero molecules

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

2

B: Glutamate receptor, ionotropic kainate 1

D: Glutamate receptor, ionotropic kainate 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	89.241, 89.241, 330.365
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	146
Space group name H-M	H3

Components on special symmetry positions

ID	Model	Components
1	1	B-463- HOH
2	1	D-397- HOH

Details

Biological dimer are generated by Chains A+C and B+D

#1: Protein	Glutamate receptor, ionotropic kainate 1 / / Glutamate receptor 5 / GluR-5 / GluR5 Mass: 29211.531 Da / Num. of mol.: 4 / Mutation: E285S Source method: isolated from a genetically manipulated source Details: Residues 1-2 are a cloning artefact. Residues 3-116 and 119-258 correspond to P 22756 residues 446-559 and 682-821, and are linked by residues 117-118. Residue 258 is engineered. Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1, Glur5 / Plasmid: pET22b (modified) / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P22756
#2: Chemical	ChemComp-NH4 / AMMONIUM ION / Ammonium Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H₄N
#3: Chemical	ChemComp-LY5 / (3S,4aR,6S,8aR)-6-{[(2S)-2-carboxy-4,4-difluoropyrrolidin-1-yl]methyl}decahydroisoquinoline-3-carboxylic acid / LY466195 Mass: 346.370 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₆H₂₄F₂N₂O₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1148 / 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: 2.17 Å³/Da / Density % sol: 43.23 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.35 Details: 20% PEG 3350, 250mM Ammonium Citrate, 2.5mM LY466195, pH 5.35, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 15, 2007
Radiation	Monochromator: Double Crystal Si-220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.58→40 Å / Num. all: 134309 / Num. obs: 134309 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.5 % / B_iso Wilson estimate: 17.13 Å² / R_merge(I) obs: 0.059 / Net I/σ(I): 14.6
Reflection shell	Resolution: 1.58→1.64 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.445 / Mean I/σ(I) obs: 3.06 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
SERGUI		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2F34

2f34

Resolution: 1.58→37.64 Å / Cor.coef. F_o:F_c: 0.969 / Cor.coef. F_o:F_c free: 0.951 / SU B: 2.966 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.085 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19948	6690	5 %	RANDOM
R_work	0.1582	-	-	-
all	0.16026	127561	-	-
obs	0.16026	127561	99.98 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 14.735 Å²

	B_aniso -1	B_aniso -2
1-	0 Å²	0 Å²
2-	-	0 Å²
3-	-	-

Refinement step

Cycle: LAST / Resolution: 1.58→37.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8069	0	110	1148	9327

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	9006
X-RAY DIFFRACTION	r_angle_refined_deg	1.614	1.99	12266
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.564	5	1149
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.808	24.433	388
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.875	15	1683
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.776	15	54
X-RAY DIFFRACTION	r_chiral_restr	0.112	0.2	1345
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	6798
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	4491
X-RAY DIFFRACTION	r_nbtor_refined	0.314	0.2	6480
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	1003
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.238	0.2	156
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.189	0.2	74
X-RAY DIFFRACTION	r_mcbond_it	1.116	1.5	5613
X-RAY DIFFRACTION	r_mcangle_it	1.647	2	8884
X-RAY DIFFRACTION	r_scbond_it	2.775	3	3896
X-RAY DIFFRACTION	r_scangle_it	4.194	4.5	3382

LS refinement shell

Resolution: 1.58→1.622 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.279	456	-
R_work	0.199	9498	-
obs	-	-	99.9 %

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	0.8865	-0.1544	0.1951	1.7992	-0.1844	1.2496	-0.0198	0.0913	0.013	-0.0626	-0.0018	-0.0768	0.08	0.0345	0.0215	0.02	0.0085	0.0046	0.0301	-0.0033	0.0308	-14.088	7.8201	-20.8126
2	0.4763	0.1732	0.1489	1.4442	0.0194	0.7913	-0.0239	-0.0419	0.0695	0.0948	-0.0125	-0.0308	-0.1277	-0.0919	0.0365	0.0342	0.0245	-0.0066	0.0465	-0.0133	0.0305	-21.9877	22.5414	-10.5382
3	0.5984	-0.5731	0.6356	1.8688	-1.0864	1.6183	-0.1041	-0.0939	-0.0433	0.1856	0.1598	-0.0209	-0.1426	-0.2103	-0.0557	0.031	0.0269	-0.0178	0.0263	-0.0088	0.0286	-18.7551	34.2812	-13.2563
4	1.8579	0.0266	-0.0555	1.0763	-0.3132	1.1701	0.0091	-0.1176	-0.0049	0.0861	-0.0485	-0.1112	0.0573	0.0629	0.0394	0.0755	0.011	-0.0115	0.0501	-0.0167	0.0569	-12.0837	9.0847	-7.0944
5	1.7955	0.001	0.5062	3.1849	-0.3139	2.2107	-0.0024	0.0043	0.0165	-0.0634	-0.0183	0.1237	0.0988	-0.2159	0.0207	0.0383	-0.0302	0.0279	0.0893	-0.0183	0.0327	-29.7537	32.8523	-74.1985
6	0.9464	-0.192	0.2933	0.9153	-0.029	1.5871	-0.0685	-0.0013	0.0824	0.0032	0.0181	-0.1081	-0.0522	-0.0519	0.0504	0.0166	-0.0076	0.0179	0.043	-0.0252	0.0295	-27.2363	39.1446	-70.9198
7	1.2534	0.0993	-0.3691	0.7583	-0.0402	1.5756	-0.0139	-0.0731	-0.0112	0.0356	0.0235	-0.0636	0.0642	0.1426	-0.0096	0.0058	0.0188	0.007	0.0446	-0.0226	0.0044	-4.9264	23.4223	-67.7172
8	1.3436	-0.124	-0.074	1.867	0.2276	1.7939	-0.1056	-0.16	-0.0577	0.0932	0.0682	0.0858	0.093	-0.0983	0.0374	0.0361	0.008	0.0111	0.0946	-0.0147	0.0001	-29.3883	32.191	-59.8576
9	1.635	0.4255	-0.1873	0.7031	-0.1744	1.5076	-0.0117	0.1161	-0.3082	0.0478	0.023	-0.1266	0.105	-0.1677	-0.0113	0.0051	-0.0173	-0.0247	0.0359	-0.0565	0.0397	-25.2974	14.2973	17.3371
10	1.7908	0.4207	0.3783	1.4562	0.4737	2.3785	0.137	0.062	-0.2118	0.0389	-0.0102	-0.2455	0.056	0.1317	-0.1268	0.0114	0.003	-0.0489	0.0084	-0.018	0.0417	-1.2573	30.8335	15.6107
11	1.6836	1.1444	-0.115	1.899	0.1287	1.0158	-0.0518	0.1429	-0.0355	0.0432	0.0281	-0.0127	-0.0337	-0.097	0.0237	0.0307	0.0123	-0.0178	0.0892	-0.0416	0.0384	-17.2045	26.3209	11.0411
12	1.7644	0.0148	-0.2675	4.2514	2.278	4.4427	0.0037	0.1218	0.0301	-0.1698	-0.0777	0.0289	-0.1838	-0.3242	0.074	0.0126	0.0329	-0.011	0.135	-0.0272	0.0106	-29.4187	24.5991	6.0995
13	0.9819	0.4061	-0.0938	1.6056	-0.1441	1.4759	-0.04	-0.0157	0.0379	0.0708	0.0103	-0.109	-0.2023	0.079	0.0298	0.0323	-0.0085	-0.0119	0.0102	-0.0007	0.0464	-15.439	46.1825	-32.5535
14	0.7182	-0.4025	-0.098	1.7256	0.2555	1.2584	-0.0291	0.0766	-0.0827	-0.0603	-0.0185	-0.0182	0.1469	-0.1074	0.0477	0.0395	-0.0244	0.0118	0.0497	-0.0039	0.0304	-23.7248	30.4818	-42.0826
15	0.2142	-0.0104	0.0879	1.5506	-0.7941	1.0566	-0.061	-0.005	-0.0114	-0.1327	0.0972	-0.0622	0.1248	-0.1469	-0.0362	0.0187	-0.0203	0.0156	0.0421	-0.0061	0.012	-19.2679	21.416	-39.9908
16	3.2747	-1.8902	1.5694	3.1569	-1.1703	2.1097	-0.0718	0.0898	0.1201	-0.3177	0.0989	-0.1118	-0.1846	0.0116	-0.0271	0.0841	-0.0527	0.0228	0.0478	0.0001	0.0404	-12.4794	44.9957	-46.9179

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	3 - 66	3 - 66
2	X-RAY DIFFRACTION	2	A	A	67 - 133	67 - 133
3	X-RAY DIFFRACTION	3	A	A	134 - 215	134 - 215
4	X-RAY DIFFRACTION	4	A	A	216 - 254	216 - 254
5	X-RAY DIFFRACTION	5	B	B	4 - 21	4 - 21
6	X-RAY DIFFRACTION	6	B	B	22 - 106	22 - 106
7	X-RAY DIFFRACTION	7	B	B	107 - 213	107 - 213
8	X-RAY DIFFRACTION	8	B	B	214 - 254	214 - 254
9	X-RAY DIFFRACTION	9	C	C	4 - 109	4 - 109
10	X-RAY DIFFRACTION	10	C	C	110 - 189	110 - 189
11	X-RAY DIFFRACTION	11	C	C	190 - 226	190 - 226
12	X-RAY DIFFRACTION	12	C	C	227 - 254	227 - 254
13	X-RAY DIFFRACTION	13	D	D	4 - 64	4 - 64
14	X-RAY DIFFRACTION	14	D	D	65 - 133	65 - 133
15	X-RAY DIFFRACTION	15	D	D	134 - 222	134 - 222
16	X-RAY DIFFRACTION	16	D	D	223 - 254	223 - 254

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