PDB-5cmk: Crystal structure of the GluK2EM LBD dimer assembly complex with ...

ID or keywords:

Entry

Database: PDB / ID: 5cmk

Title

Crystal structure of the GluK2EM LBD dimer assembly complex with glutamate and LY466195

Components

Glutamate receptor ionotropic, kainate 2

Keywords

TRANSPORT PROTEIN / Membrane 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 / negative regulation of synaptic transmission, glutamatergic / 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: 1.801 Å

Authors

Chittori, S. / Mayer, M.L.

Citation

Journal: Nature / Year: 2016
Title: Structural basis of kainate subtype glutamate receptor desensitization.
Authors: Joel R Meyerson / Sagar Chittori / Alan Merk / Prashant Rao / Tae Hee Han / Mihaela Serpe / Mark L Mayer / Sriram Subramaniam /

Abstract: Glutamate receptors are ligand-gated tetrameric ion channels that mediate synaptic transmission in the central nervous system. They are instrumental in vertebrate cognition and their dysfunction ...

History

Deposition	Jul 16, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 7, 2016	Group: Database references
Revision 1.2	Sep 14, 2016	Group: Database references
Revision 1.3	Oct 5, 2016	Group: Database references
Revision 1.4	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5cmk.cif.gz	316.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5cmk.ent.gz	263.8 KB	Display	PDB format
PDBx/mmJSON format	5cmk.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/cm/5cmk ftp://data.pdbj.org/pub/pdb/validation_reports/cm/5cmk	HTTPS FTP

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Related structure data

Related structure data	8289C 8290C 5cmmC 5kufC 5kuhC 3g3fS 2qs4 4uqq S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4h8i-d 2anj-1 4ymb-d 2i0b-2 3c36-d 3c31-d 5zg2-d 3en3-1 2gfe-1 4o3b-d 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) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #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

59.5 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)	102.759, 102.759, 281.992
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	178
Space group name H-M	P6₁22

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Protein , 1 types, 2 molecules AB

#1: Protein	Glutamate receptor ionotropic, kainate 2 / GluK2 / Glutamate receptor 6 / GluR6 Mass: 29356.621 Da / Num. of mol.: 2 / Fragment: UNP residues 429-544, 667-806 / Mutation: A487T A658S N690S F704L,A487T A658S N690S F704L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik2, Glur6 / Plasmid: PET22 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: P42260

#1: Protein

Glutamate receptor ionotropic, kainate 2 / GluK2 / Glutamate receptor 6 / GluR6

Mass: 29356.621 Da / Num. of mol.: 2 / Fragment: UNP residues 429-544, 667-806 / Mutation: A487T A658S N690S F704L,A487T A658S N690S F704L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Rattus norvegicus (Norway rat) / Gene: Grik2, Glur6 / Plasmid: PET22 / Production host:

Escherichia coli (E. coli) / Strain (production host): Origami B(DE3) / References: UniProt: P42260

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Non-polymers , 6 types, 541 molecules

#2: Chemical	ChemComp-GLU / GLUTAMIC ACID Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₉NO₄
#3: Chemical	ChemComp-LI / LITHIUM ION Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: 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.: 1 / Source method: obtained synthetically / Formula: C₁₆H₂₄F₂N₂O₄
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 533 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.66 Å³/Da / Density % sol: 66.44 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Reservoir: 2M Li2SO4 3% PEG 4K 0.1M MgSO4 0.1 M NaAcetate Protein buffer: 100 mM NaCl, 5 mM LY466195, 1 mM EDTA, 10 mM HEPES pH 7 No added glutamate PH range: 5.5

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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: RAYONIX MX300-HS / Detector: CCD / Date: Jul 1, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. obs: 82330 / % possible obs: 100 % / Redundancy: 14.5 % / R_merge(I) obs: 0.058 / Net I/σ(I): 48.4
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 14.2 % / R_merge(I) obs: 1 / Mean I/σ(I) obs: 2.8 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3G3F

3g3f

Resolution: 1.801→29.864 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0.09 / Phase error: 17.35 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1869	4135	5.04 %	Random selection
R_work	0.1636	-	-	-
obs	0.1648	82330	99.9 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.801→29.864 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4030	0	48	533	4611

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	4252
X-RAY DIFFRACTION	f_angle_d	1.403	5750
X-RAY DIFFRACTION	f_dihedral_angle_d	13.797	1623
X-RAY DIFFRACTION	f_chiral_restr	0.068	638
X-RAY DIFFRACTION	f_plane_restr	0.007	727

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 (%)
1.8006-1.8211	0.248	260	0.2328	4753	X-RAY DIFFRACTION	98
1.8211-1.8425	0.2495	256	0.2257	4839	X-RAY DIFFRACTION	99
1.8425-1.865	0.2193	237	0.2115	4929	X-RAY DIFFRACTION	100
1.865-1.8886	0.2156	232	0.2002	4878	X-RAY DIFFRACTION	100
1.8886-1.9134	0.2383	246	0.2025	4891	X-RAY DIFFRACTION	100
1.9134-1.9396	0.2204	284	0.1905	4917	X-RAY DIFFRACTION	100
1.9396-1.9673	0.1884	245	0.1842	4828	X-RAY DIFFRACTION	100
1.9673-1.9967	0.2088	248	0.1821	4917	X-RAY DIFFRACTION	100
1.9967-2.0279	0.1786	267	0.1811	4881	X-RAY DIFFRACTION	100
2.0279-2.0611	0.2229	257	0.1696	4864	X-RAY DIFFRACTION	100
2.0611-2.0966	0.1893	241	0.1694	4927	X-RAY DIFFRACTION	100
2.0966-2.1348	0.1704	240	0.1671	4856	X-RAY DIFFRACTION	100
2.1348-2.1758	0.178	243	0.1659	4935	X-RAY DIFFRACTION	100
2.1758-2.2202	0.2059	260	0.162	4846	X-RAY DIFFRACTION	100
2.2202-2.2685	0.1764	257	0.1594	4895	X-RAY DIFFRACTION	100
2.2685-2.3212	0.174	247	0.1553	4863	X-RAY DIFFRACTION	100
2.3212-2.3792	0.1973	246	0.167	4904	X-RAY DIFFRACTION	100
2.3792-2.4435	0.2148	221	0.1732	4944	X-RAY DIFFRACTION	100
2.4435-2.5154	0.1988	269	0.1686	4864	X-RAY DIFFRACTION	100
2.5154-2.5966	0.1901	282	0.1615	4830	X-RAY DIFFRACTION	100
2.5966-2.6893	0.2029	279	0.1699	4877	X-RAY DIFFRACTION	100
2.6893-2.7969	0.2145	277	0.1776	4849	X-RAY DIFFRACTION	100
2.7969-2.9241	0.2087	298	0.1709	4875	X-RAY DIFFRACTION	100
2.9241-3.0781	0.1988	260	0.1724	4840	X-RAY DIFFRACTION	100
3.0781-3.2707	0.1704	269	0.1712	4884	X-RAY DIFFRACTION	100
3.2707-3.5229	0.1867	326	0.1621	4820	X-RAY DIFFRACTION	100
3.5229-3.8768	0.1687	251	0.1427	4886	X-RAY DIFFRACTION	100
3.8768-4.4362	0.1461	267	0.1189	4883	X-RAY DIFFRACTION	100
4.4362-5.5831	0.155	263	0.1287	4860	X-RAY DIFFRACTION	100
5.5831-29.8678	0.1776	234	0.1746	4910	X-RAY DIFFRACTION	100

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	0.01	0.0017	-0.0076	0.0048	0.0001	0.0063	-0.0117	-0.0196	0.0085	0.0081	-0.0356	0.0256	-0.005	-0.0123	-0.0033	0.1326	-0.0174	-0.0244	0.1196	-0.0623	0.1292	31.6944	-11.5754	61.7468
2	0.0134	-0.0054	0.0001	0.0166	-0.002	0.0004	-0.0182	0.0027	0.0134	-0.0091	0.0067	0.0028	-0.0202	0.0024	-0.0253	0.1217	-0.0352	-0.0367	0.0926	-0.0574	0.0966	37.3447	-9.9257	58.461
3	0.0048	-0.011	0.0057	0.0276	-0.0098	0.0163	-0.0322	-0.0383	0.0583	0.0089	-0.0467	0.0741	-0.0334	-0.1045	-0.0128	0.0955	-0.0044	-0.0279	0.1984	-0.1352	0.1859	17.3635	-13.5309	58.867
4	0.0161	0.0038	0.0184	0.0063	-0.0013	0.0273	0.0436	-0.0439	-0.057	0.0448	-0.0066	0.0104	0.0325	-0.0676	0.0015	0.2676	-0.1612	0.0644	0.3142	-0.0682	0.2129	17.6194	-34.5701	72.1558
5	0.0074	0.0026	-0.0051	0.0009	-0.0018	0.0035	0.0021	-0.0069	-0.0049	0.0042	0.001	0.0113	0.004	-0.0149	-0.001	0.2529	-0.1702	0.0817	0.4532	-0.0844	0.3202	8.0321	-30.2876	68.9832
6	0.0721	-0.0248	-0.0588	0.0278	-0.0036	0.0815	-0.0175	-0.0459	-0.0006	0.0773	-0.1064	0.0502	0.0207	-0.1264	-0.124	0.164	-0.0675	-0.0145	0.1529	-0.0622	0.1358	24.2177	-27.1535	67.9339
7	0.0002	0.0011	-0	0.0049	-0.0003	0.0001	-0.0195	0.0172	-0.0084	-0.0085	0.0048	-0.0037	-0.0213	0.0024	-0.0241	0.1349	-0.0302	-0.0452	0.1511	-0.0572	0.1253	28.0729	-16.793	43.9436
8	0.0019	-0.0016	0.0005	0.0015	-0.0009	0.0009	0.0092	0.0118	-0.0162	-0.0003	0.0018	-0.0016	0.0051	0.0048	-0.0007	0.1351	0.0018	-0.0513	0.1604	-0.0586	0.1764	38.1794	-25.2308	54.3902
9	0.0261	-0.0002	0.0066	0.0078	-0.0221	0.0633	0.0047	-0.0328	0.0196	-0.0192	-0.025	0.0368	-0.0031	-0.0445	-0.0179	0.0986	-0.0225	-0.0587	0.1423	-0.04	0.1216	6.283	-36.9855	32.6406
10	0.0089	-0.0015	0.0013	0.0005	0.0018	0.0127	-0.0162	-0.0145	0.0259	-0.0113	-0.0008	0.022	-0.019	-0.0162	-0.0023	0.1028	0.0252	-0.0546	0.1928	-0.0897	0.1584	6.8041	-29.3195	33.1284
11	0.0297	-0.0147	-0.0196	0.0982	0.0661	0.0872	-0.0181	-0.0404	0.0013	-0.0517	0.0103	-0.0721	-0.0685	0.0184	-0.0383	0.0977	-0.0285	-0.0512	0.1384	-0.0294	0.1329	27.6966	-32.1211	36.6591
12	0.0151	0.0059	-0.0023	0.0053	-0.0045	0.0047	0.0082	-0.0094	0.0202	-0.0179	0.0104	-0.0541	-0.0129	0.0199	0.0101	0.1757	-0.0662	0.1068	0.1717	-0.0675	0.379	41.2233	-38.417	35.4941
13	0.0039	0.0011	0.0046	0.0034	0.0052	0.0099	-0.047	-0.0084	0.0116	-0.0199	-0.0252	-0.0292	0.0334	-0.0031	-0.0044	0.1801	-0.0284	0.0662	0.1356	0.0179	0.1992	32.2563	-49.9432	35.1454
14	0.1211	-0.0096	-0.1134	0.0612	-0.003	0.11	-0.0363	-0.1075	0.0509	0.0083	-0.0507	0.0162	-0.0344	0.0031	-0.0765	0.1045	-0.0302	-0.0503	0.1261	-0.0046	0.0936	24.1286	-39.5084	42.9462
15	0.0184	0.0082	-0.0235	0.0041	-0.0133	0.0499	-0.0166	-0.0383	0.0146	-0.0003	-0.0451	0.0304	-0.0204	-0.0151	-0.0245	0.1275	-0.0321	-0.0143	0.2553	-0.1114	0.1804	10.0388	-23.7667	46.9365
16	0.0015	0.0009	-0.0005	0.0009	-0	0.0003	-0.0211	-0.0159	-0.0029	-0.0032	-0.0158	0.0035	0.0101	-0.0032	0	0.1247	-0.0679	-0.002	0.2215	-0.0208	0.1555	12.1631	-41.2255	47.1998

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 3:21)
2	X-RAY DIFFRACTION	2	(chain A and resid 22:53)
3	X-RAY DIFFRACTION	3	(chain A and resid 54:109)
4	X-RAY DIFFRACTION	4	(chain A and resid 110:145)
5	X-RAY DIFFRACTION	5	(chain A and resid 146:166)
6	X-RAY DIFFRACTION	6	(chain A and resid 167:226)
7	X-RAY DIFFRACTION	7	(chain A and resid 227:240)
8	X-RAY DIFFRACTION	8	(chain A and resid 241:253)
9	X-RAY DIFFRACTION	9	(chain B and resid 2:40)
10	X-RAY DIFFRACTION	10	(chain B and resid 41:60)
11	X-RAY DIFFRACTION	11	(chain B and resid 61:137)
12	X-RAY DIFFRACTION	12	(chain B and resid 138:171)
13	X-RAY DIFFRACTION	13	(chain B and resid 172:190)
14	X-RAY DIFFRACTION	14	(chain B and resid 191:225)
15	X-RAY DIFFRACTION	15	(chain B and resid 226:242)
16	X-RAY DIFFRACTION	16	(chain B and resid 243:254)

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