PDB-8r32: Crystal structure of the GluK2 ligand-binding domain in complex w...

ID or keywords:

Entry

Database: PDB / ID: 8r32

Title

Crystal structure of the GluK2 ligand-binding domain in complex with L-glutamate and BPAM344 at 1.60 A resolution

Components

Glutamate receptor ionotropic, kainate 2

Keywords

MEMBRANE PROTEIN / IONOTROPIC GLUTAMATE RECEPTOR / GLUK2 LIGAND-BINDING DOMAIN / POSITIVE ALLOSTERIC MODULATOR / L-glutamate

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

Bay, Y. / Jeppesen, M.E. / Frydenvang, K. / Kastrup, J.S.

Funding support

3items

Citation

Journal: Febs Lett. / Year: 2024
Title: The positive allosteric modulator BPAM344 and L-glutamate introduce an active-like structure of the ligand-binding domain of GluK2.
Authors: Bay, Y. / Egeberg Jeppesen, M. / Frydenvang, K. / Francotte, P. / Pirotte, B. / Pickering, D.S. / Kristensen, A.S. / Kastrup, J.S.

History

Deposition	Nov 8, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 18, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8r32.cif.gz	324.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8r32.ent.gz	267.9 KB	Display	PDB format
PDBx/mmJSON format	8r32.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8r32_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	8r32_full_validation.pdf.gz	1.6 MB	Display
Data in XML	8r32_validation.xml.gz	30.8 KB	Display
Data in CIF	8r32_validation.cif.gz	43.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r3/8r32 ftp://data.pdbj.org/pub/pdb/validation_reports/r3/8r32	HTTPS FTP

-
Related structure data

Related structure data	2xxrS S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#235 - Jul 2019 AMPA Receptor similarity (14) #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

A: Glutamate receptor ionotropic, kainate 2

hetero molecules

A: Glutamate receptor ionotropic, kainate 2

hetero molecules

defined by author&software
Evidence: Chain A generates a dimer with a symmetry-related Chain A.
59.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Glutamate receptor ionotropic, kainate 2

hetero molecules

B: Glutamate receptor ionotropic, kainate 2

hetero molecules

defined by author&software
Evidence: Chain B generates a dimer with a symmetry-related Chain B.
59.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	98.197, 100.746, 48.160
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-903- CL
2	1	B-903- CL

-
Protein , 1 types, 2 molecules AB

#1: Protein	Glutamate receptor ionotropic, kainate 2 / GluK2 / Glutamate receptor 6 / GluR-6 / GluR6 Mass: 29242.520 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK2. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 545 AND 546 OF THE ...Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK2. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 545 AND 546 OF THE STRUCTURE). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (429-544, 667-805). RESIDUE 428 IS A REMNANT FROM CLONING. Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grik2, Glur6 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P42260

#1: Protein

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

Mass: 29242.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK2. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 545 AND 546 OF THE ...
Source: (gene. exp.)

Rattus norvegicus (Norway rat) / Gene: Grik2, Glur6 / Plasmid: pET-28a / Production host:

Escherichia coli (E. coli) / Strain (production host): Origami 2 / References: UniProt: P42260

-
Non-polymers , 5 types, 555 molecules

#2: Chemical	ChemComp-GLU / GLUTAMIC ACID Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₉NO₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-2J9 / 4-cyclopropyl-7-fluoro-3,4-dihydro-2H-1,2,4-benzothiadiazine 1,1-dioxide Mass: 242.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₁FN₂O₂S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 544 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.04 Å³/Da / Density % sol: 39.61 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 25% PEG4000, 9% propan-2-ol, 0.1 mM sodium acetate, pH 5.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 28, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.6→48.16 Å / Num. obs: 63898 / % possible obs: 100 % / Redundancy: 13.6 % / CC_1/2: 0.999 / R_merge(I) obs: 0.112 / R_pim(I) all: 0.031 / R_rim(I) all: 0.117 / Χ²: 1 / Net I/σ(I): 16.3 / Num. measured all: 869168
Reflection shell	Resolution: 1.6→1.63 Å / % possible obs: 99.9 % / Redundancy: 13.6 % / R_merge(I) obs: 0.789 / Num. measured all: 41810 / Num. unique obs: 3075 / CC_1/2: 0.91 / R_pim(I) all: 0.218 / R_rim(I) all: 0.819 / Χ²: 1.05 / Net I/σ(I) obs: 3.9

-
Processing

Software

Name	Version	Classification
PHENIX	(1.20_4459: ???)	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2xxr

2xxr

Resolution: 1.6→48.16 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0.96 / Phase error: 16.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1785	3201	5.02 %
R_work	0.1525	-	-
obs	0.1538	63827	99.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.6→48.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4028	0	59	544	4631

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4345
X-RAY DIFFRACTION	f_angle_d	1.032	5896
X-RAY DIFFRACTION	f_dihedral_angle_d	6.208	625
X-RAY DIFFRACTION	f_chiral_restr	0.063	648
X-RAY DIFFRACTION	f_plane_restr	0.009	743

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 (%)
1.6-1.62	0.27	129	0.2308	2572	X-RAY DIFFRACTION	100
1.62-1.65	0.2225	137	0.1994	2606	X-RAY DIFFRACTION	100
1.65-1.68	0.2176	142	0.1924	2591	X-RAY DIFFRACTION	100
1.68-1.71	0.2372	153	0.1871	2567	X-RAY DIFFRACTION	100
1.71-1.74	0.1999	126	0.1666	2634	X-RAY DIFFRACTION	100
1.74-1.77	0.1839	132	0.1568	2622	X-RAY DIFFRACTION	100
1.77-1.81	0.2113	124	0.1583	2601	X-RAY DIFFRACTION	100
1.81-1.84	0.2048	158	0.1606	2583	X-RAY DIFFRACTION	100
1.84-1.89	0.1815	116	0.166	2626	X-RAY DIFFRACTION	100
1.89-1.94	0.214	139	0.1675	2651	X-RAY DIFFRACTION	100
1.94-1.99	0.2011	130	0.164	2609	X-RAY DIFFRACTION	100
1.99-2.05	0.1841	176	0.1504	2563	X-RAY DIFFRACTION	100
2.05-2.11	0.1808	149	0.142	2627	X-RAY DIFFRACTION	100
2.11-2.19	0.1535	147	0.1318	2638	X-RAY DIFFRACTION	100
2.19-2.28	0.173	144	0.1335	2601	X-RAY DIFFRACTION	100
2.28-2.38	0.163	119	0.1391	2654	X-RAY DIFFRACTION	100
2.38-2.5	0.1775	126	0.1466	2640	X-RAY DIFFRACTION	100
2.5-2.66	0.1598	118	0.1493	2695	X-RAY DIFFRACTION	100
2.66-2.87	0.2022	142	0.1464	2647	X-RAY DIFFRACTION	100
2.87-3.15	0.1681	144	0.148	2647	X-RAY DIFFRACTION	100
3.15-3.61	0.1641	140	0.1409	2704	X-RAY DIFFRACTION	100
3.61-4.55	0.1332	142	0.1326	2704	X-RAY DIFFRACTION	100
4.55-48.16	0.1895	168	0.1746	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	1.0664	0.5861	0.1095	1.9382	0.5081	1.0095	-0.0347	0.1242	0.1493	-0.1397	0.048	0.2147	-0.1362	-0.0534	-0.0157	0.0957	0.002	-0.0194	0.1018	0.0331	0.1068	30.6248	7.004	-8.2094
2	0.6669	0.2944	-0.3927	1.0247	-0.5829	1.6874	-0.0088	-0.0082	-0.0202	0.0291	0.0308	0.0161	-0.009	-0.0099	-0.0252	0.0545	0.0025	-0.0061	0.0623	-0.0089	0.0819	36.507	-6.2505	2.7283
3	1.7064	0.1195	-0.6331	2.6909	-0.0137	2.4496	-0.0629	0.1123	-0.072	0.0347	0.0619	0.2446	0.1397	-0.1695	0.0096	0.0698	-0.0051	-0.0054	0.0799	0.0105	0.0879	29.7761	-10.0997	6.8499
4	0.8723	0.3272	-0.3557	1.5053	-0.2143	0.4529	0.0335	-0.0257	0.0632	0.1041	-0.0066	-0.0255	-0.0803	0.0187	-0.06	0.0798	-0.0018	-0.0046	0.0873	-0.0066	0.0858	42.016	6.7341	1.6137
5	1.431	-0.0097	-0.4309	1.0248	0.3718	1.7882	0.0668	0.015	0.1602	-0.1572	0.1975	-0.514	-0.2651	0.3219	-0.1959	0.1207	-0.0244	0.0377	0.1448	-0.0578	0.2591	15.7413	15.4471	-26.69
6	4.3817	-1.4262	-1.3471	2.3384	0.6357	0.7915	0.1121	0.2734	0.5068	-0.3371	0.0574	-0.2734	-0.1996	0.0158	-0.1897	0.1364	-0.0177	0.0366	0.1061	0.0189	0.1503	6.5452	19.5306	-32.1519
7	1.1198	-0.5016	-0.2307	1.4133	0.2133	1.3529	0.0616	0.1388	0.136	-0.1738	-0.0425	-0.0329	-0.182	-0.0808	-0.0152	0.0863	0.0156	-0.0024	0.0713	0.0098	0.0856	-1.9411	13.6713	-28.6828
8	3.3245	-0.0622	4.5783	4.631	-0.2046	6.7822	-0.1065	-0.6903	-0.0833	0.6832	0.1681	0.2982	0.4083	-0.0776	-0.0682	0.2	0.039	0.061	0.2264	-0.0186	0.0977	-13.8202	17.0604	-2.7242
9	4.3469	0.6951	-1.1077	4.8709	1.0648	4.2532	-0.0992	0.1821	0.0039	-0.1382	0.0875	-0.055	-0.0329	-0.1998	0.0226	0.0606	0.0375	-0.0036	0.0503	0.0227	0.0444	-11.367	17.9335	-19.6842
10	6.7122	4.3533	2.1042	2.9611	1.76	1.8159	-0.1824	-0.0857	0.4401	-0.1198	0.0123	0.3876	-0.202	-0.146	0.1049	0.1088	0.0371	0.0153	0.1184	-0.0131	0.1031	-15.974	22.0059	-15.9257
11	2.7488	-0.7602	-0.2143	2.9543	1.8331	2.2241	-0.0726	-0.1311	0.2036	0.1069	0.2235	-0.2669	-0.0488	0.1957	-0.1079	0.0903	0.0055	-0.0134	0.0787	-0.0322	0.1056	-0.9908	20.7906	-11.1249
12	1.0847	-0.1339	0.0121	0.2003	0.6776	2.857	-0.2116	-0.3943	0.206	0.2943	0.1666	-0.1218	-0.0377	0.2713	0.0351	0.2008	0.0606	-0.054	0.2013	-0.0452	0.1452	-0.3413	11.8562	-9.3811
13	1.6635	-2.6616	1.6179	5.1798	-3.2383	4.4828	0.1574	0.1802	-0.0795	-0.3113	-0.1012	0.091	0.192	0.0332	-0.0668	0.0529	-0.0067	0.0085	0.0805	-0.0075	0.0754	7.5648	1.771	-32.7467
14	2.5273	0.7648	-1.3925	1.667	-0.0596	3.7666	-0.1188	-0.4165	0.2264	0.4277	0.2782	-0.4705	-0.0968	0.3583	-0.1938	0.1546	0.045	-0.092	0.1954	-0.0407	0.1919	14.0146	6.1567	-12.972

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 430 through 506 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 507 through 680 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 681 through 748 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 749 through 805 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 431 through 474 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 475 through 492 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 493 through 543 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 544 through 680 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 681 through 699 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 700 through 716 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 717 through 746 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 747 through 764 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 765 through 787 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 788 through 805 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 555 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 555 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 555 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi