PDB-8r36: Crystal structure of the Gluk1 ligand-binding domain in complex w...

ID or keywords:

Entry

Database: PDB / ID: 8r36

Title

Crystal structure of the Gluk1 ligand-binding domain in complex with kainate and BPAM538 at 1.90 A resolution

Components

Glutamate receptor ionotropic, kainate 1

Keywords

MEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / GLUK1 LIGAND-BINDING DOMAIN / POSITIVE ALLOSTERIC MODULATOR / KAINATE

Function / homology

Function and homology information

negative regulation of synaptic transmission, GABAergic / gamma-aminobutyric acid secretion / 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 / regulation of short-term neuronal synaptic plasticity / negative regulation of synaptic transmission, glutamatergic / glutamate binding ...
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Bay, Y. / Frantsen, S.M. / Frydenvang, K. / Kastrup, J.S.

Funding support

Denmark,

Sweden, 4items

Citation

Journal: J.Struct.Biol. / Year: 2024
Title: Crystal structure of the GluK1 ligand-binding domain with kainate and the full-spanning positive allosteric modulator BPAM538.
Authors: Bay, Y. / Cabello, F.J.M. / Koens, C.C. / Frantsen, S.M. / Pickering, D.S. / Frydenvang, K. / Francotte, P. / Pirotte, B. / Kristensen, A.S. / Bowie, D. / Kastrup, J.S.

History

Deposition	Nov 8, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 14, 2024	Provider: repository / Type: Initial release
Revision 1.1	Sep 4, 2024	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8r36.cif.gz	231.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8r36.ent.gz	184.3 KB	Display	PDB format
PDBx/mmJSON format	8r36.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	8r36_validation.pdf.gz	372.8 KB	Display	wwPDB validaton report
Full document	8r36_full_validation.pdf.gz	373.3 KB	Display
Data in XML	8r36_validation.xml.gz	2 KB	Display
Data in CIF	8r36_validation.cif.gz	9.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r3/8r36 ftp://data.pdbj.org/pub/pdb/validation_reports/r3/8r36	HTTPS FTP

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Related structure data

Related structure data	4e0xS S: Starting model for refinement
Similar structure data	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 (12) #199 - Jul 2016 Monellin similarity (2)

Deposited unit

A: Glutamate receptor ionotropic, kainate 1

B: Glutamate receptor ionotropic, kainate 1

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	71.485, 71.485, 232.902
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

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Protein , 1 types, 2 molecules AB

#1: Protein	Glutamate receptor ionotropic, kainate 1 / GluK1 / Glutamate receptor 5 / GluR-5 / GluR5 Mass: 29108.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 117 AND 118 OF THE ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 117 AND 118 OF THE STRUCTURE). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (2-116, 119-257). RESIDUE 1 IS A REMNANT FROM CLONING. THIS RESIDUE NUMBERING IS ISOFORM GLUR5-2 OF P22756 IN UNP. THE CONFLICT OF GLY 34 IS REFERED TO ALA -> GLY SEQUENCE CONFLICT AT RESIDUE 462 IN UNP DATABASE. Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik1, Glur5 / Plasmid: pET28A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI 2 / References: UniProt: P22756

#1: Protein

Glutamate receptor ionotropic, kainate 1 / GluK1 / Glutamate receptor 5 / GluR-5 / GluR5

Mass: 29108.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 117 AND 118 OF THE ...
Source: (gene. exp.)

Rattus norvegicus (Norway rat) / Gene: Grik1, Glur5 / Plasmid: pET28A(+) / Production host:

Escherichia coli (E. coli) / Strain (production host): ORIGAMI 2 / References: UniProt: P22756

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Non-polymers , 6 types, 376 molecules

#2: Chemical	ChemComp-KAI / 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE / KAINATE Mass: 213.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅NO₄ / Comment: neurotransmitter, agonist*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-9TE / 4-cyclopropyl-7-(3-methoxyphenoxy)-2,3-dihydro-1$l^{6},2,4-benzothiadiazine 1,1-dioxide Mass: 346.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₁₈N₂O₄S / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.56 Å³/Da / Density % sol: 51.87 %
Crystal grow	Temperature: 279 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 15.2% PEG4000, 0.3 M lithium sulfate, and 0.1 M sodium acetate pH 5.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9762 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 7, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 1.9→49.4 Å / Num. obs: 48841 / % possible obs: 100 % / Redundancy: 26.4 % / CC_1/2: 0.999 / R_merge(I) obs: 0.087 / R_pim(I) all: 0.017 / R_rim(I) all: 0.089 / Net I/σ(I): 23.4 / Num. measured all: 1291136
Reflection shell	Resolution: 1.9→2 Å / % possible obs: 100 % / Redundancy: 26.6 % / R_merge(I) obs: 0.457 / Num. measured all: 186128 / Num. unique obs: 6995 / CC_1/2: 0.989 / R_pim(I) all: 0.089 / R_rim(I) all: 0.465 / Net I/σ(I) obs: 7.7

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
SCALA		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4E0X

4e0x

Resolution: 1.9→46.37 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0.7 / Phase error: 18.14 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1993	2451	5.03 %
R_work	0.1642	-	-
obs	0.1659	48706	99.92 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.9→46.37 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4050	0	106	357	4513

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4308
X-RAY DIFFRACTION	f_angle_d	0.808	5836
X-RAY DIFFRACTION	f_dihedral_angle_d	14.738	1667
X-RAY DIFFRACTION	f_chiral_restr	0.055	642
X-RAY DIFFRACTION	f_plane_restr	0.006	731

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 (%)
1.9-1.94	0.267	123	0.2055	2539	X-RAY DIFFRACTION	100
1.94-1.98	0.2037	135	0.1878	2498	X-RAY DIFFRACTION	100
1.98-2.02	0.2188	115	0.1716	2534	X-RAY DIFFRACTION	100
2.02-2.07	0.2016	124	0.164	2522	X-RAY DIFFRACTION	100
2.07-2.12	0.2142	141	0.1623	2515	X-RAY DIFFRACTION	100
2.12-2.17	0.232	132	0.1662	2539	X-RAY DIFFRACTION	100
2.17-2.24	0.1812	128	0.1662	2548	X-RAY DIFFRACTION	100
2.24-2.31	0.1896	126	0.1632	2535	X-RAY DIFFRACTION	100
2.31-2.39	0.1938	131	0.1532	2539	X-RAY DIFFRACTION	100
2.39-2.49	0.1986	143	0.1609	2526	X-RAY DIFFRACTION	100
2.49-2.6	0.2018	169	0.1585	2523	X-RAY DIFFRACTION	100
2.6-2.74	0.1914	131	0.1638	2578	X-RAY DIFFRACTION	100
2.74-2.91	0.2275	125	0.1803	2578	X-RAY DIFFRACTION	100
2.91-3.14	0.2352	158	0.1734	2575	X-RAY DIFFRACTION	100
3.14-3.45	0.2174	138	0.1601	2576	X-RAY DIFFRACTION	100
3.45-3.95	0.1611	158	0.1493	2620	X-RAY DIFFRACTION	100
3.95-4.98	0.1696	136	0.1358	2666	X-RAY DIFFRACTION	100
4.98-46.37	0.2158	138	0.1963	2844	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	4.1094	-0.8637	0.0681	3.5109	2.0431	4.8841	0.0101	0.1784	-0.6801	-0.68	0.179	-0.3911	0.367	0.2053	-0.1154	0.3909	0.0282	0.0332	0.1906	-0.044	0.288	-2.4913	21.9945	-16.7576
2	3.6979	-0.8305	-0.6931	2.4535	4.2336	7.7003	-0.1061	0.3327	-0.3502	-0.5166	0.1254	-0.3826	0.368	0.2842	0.0142	0.5325	0.0564	0.1051	0.2013	-0.0237	0.358	0.7986	16.1303	-15.2462
3	1.8633	0.5509	0.0681	1.8331	-0.1759	1.5998	-0.0315	0.0811	-0.1025	-0.2014	0.011	0.1448	0.2468	-0.1745	0.0113	0.251	-0.0199	0.0128	0.1671	-0.0106	0.1625	-9.7574	31.6169	-12.6838
4	7.3061	1.1958	-1.4329	4.1387	-1.1224	3.5938	0.1226	-0.012	0.5818	0.0147	0.0323	0.0333	-0.4136	0.1252	-0.0959	0.2884	-0.0345	0.0231	0.1682	-0.0307	0.2126	2.3478	51.5106	-12.7264
5	6.4546	-2.4796	-1.1746	8.5472	2.6063	5.8195	0.1683	0.4976	0.3991	-0.2882	-0.2227	0.3503	-0.4581	-0.3387	0.0377	0.2128	-0.0245	0.0281	0.1787	0.0553	0.2507	-2.2478	52.6552	-17.8483
6	2.3087	2.5236	-2.4846	4.6687	-4.399	5.1236	-0.018	-0.1086	-0.1456	-0.1908	-0.1458	-0.2134	0.1479	0.4613	0.1511	0.1712	0.0091	-0.0121	0.2469	-0.0264	0.2131	8.5551	40.9489	-14.2019
7	3.4492	-1.2822	0.6333	3.245	-1.5324	3.2142	-0.1006	-0.2733	-0.5171	0.1025	0.0397	-0.2448	0.2843	0.2467	0.0639	0.3537	0.0274	0.0341	0.1306	-0.0548	0.2115	-0.4784	23.822	-2.9026
8	2.5693	-2.4637	-2.7965	3.554	1.0076	5.4473	0.0444	-0.2504	0.1478	0.1529	0.2331	-0.1307	-0.2186	0.0893	-0.2451	0.1948	-0.0344	0.0071	0.1902	-0.0414	0.2376	-12.9772	46.1515	19.8656
9	2.0266	0.0521	0.7016	0.9854	-0.2896	2.4664	0.0511	-0.075	-0.0577	0.0316	-0.0687	-0.0706	0.236	0.3373	0.0199	0.2421	0.0157	0.0347	0.2395	-0.0088	0.2	0.9146	33.1142	15.8007

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 20
2	X-RAY DIFFRACTION	2	A	21 - 47
3	X-RAY DIFFRACTION	3	A	48 - 115
4	X-RAY DIFFRACTION	4	A	116 - 151
5	X-RAY DIFFRACTION	5	A	152 - 172
6	X-RAY DIFFRACTION	6	A	173 - 216
7	X-RAY DIFFRACTION	7	A	217 - 256
8	X-RAY DIFFRACTION	8	B	4 - 47
9	X-RAY DIFFRACTION	9	B	48 - 257

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