9DHR: Isoform Flip of Glutamate receptor 2

Glutamate activated state of the GluA2-gamma2 complex. Determined by electron microscopy at 3.54 Å resolution. Released 26 Mar 2025.

Method: Electron microscopy
Resolution: 3.54 Å
Organisms: Rattus norvegicus, Mus musculus
Chains: 8
Atoms: 18,298
Mol. weight: 282.87 kDa
Ligands: GLU
Released: 26 Mar 2025

Explore 9DHR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9DHR contains 119 α-helices and 103 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 24 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	392-394	3
β-strand	395-396	2	1
β-strand	397-398	2	2
β-strand	407-408	2	3
α-helix	417-420	4
β-strand	421-422	2	3
α-helix	424-436	13
β-strand	440-441	2	1
β-strand	453	1	4
β-strand	460	1	4
α-helix	462-468	7
β-strand	474-475	2	2
β-strand	480	1	5
α-helix	485-487	3
β-strand	489-491	3	2
α-helix	492	1
α-helix	494	1
β-strand	497-498	2	6
β-strand	500-505	6	7
α-helix	516-518	3
α-helix	523-544	22
α-helix	566-568	3
α-helix	573-584	12
α-helix	596-623	28
α-helix	633	1
α-helix	634-640	7
β-strand	646-648	3	7
β-strand	650	1	8
α-helix	654-661	8
α-helix	665-674	10
β-strand	683	1	8
α-helix	686-695	10
β-strand	700-705	6	7
α-helix	706-714	9
β-strand	720-723	4	7
β-strand	730-731	2	6
β-strand	732	1	5
β-strand	735-737	3	2
α-helix	743-755	13
α-helix	758-766	9
α-helix	785-786	2
β-strand	787	1	9
α-helix	788	1
α-helix	789-791	3
α-helix	793-819	27

Chain B: 23 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	395-399	5	10
β-strand	402	1	11
β-strand	406	1	11
β-strand	407-408	2	12
α-helix	410-413	4
α-helix	417-420	4
β-strand	421-422	2	12
α-helix	424-436	13
β-strand	440-444	5	10
β-strand	453	1	13
α-helix	454	1
β-strand	460	1	13
α-helix	462-468	7
β-strand	474-475	2	10
β-strand	480	1	14
α-helix	483-486	4
β-strand	489-491	3	10
α-helix	492	1
α-helix	494	1
β-strand	496-498	3	14
β-strand	500-505	6	15
α-helix	516-518	3
β-strand	521	1	16
α-helix	523-543	21
α-helix	573-584	12
α-helix	596-613	18
α-helix	621-624	4
α-helix	638-640	3
β-strand	646-648	3	15
β-strand	650	1	17
α-helix	654-661	8
α-helix	665-674	10
β-strand	683	1	17
α-helix	686-695	10
β-strand	700-705	6	15
α-helix	706-712	7
β-strand	720-723	4	15
β-strand	730-732	3	14
β-strand	735-737	3	10
α-helix	743-756	14
α-helix	758-767	10
α-helix	782-785	4
α-helix	789-791	3
α-helix	794-817	24

Chain C: 23 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	393-394	2
β-strand	395-396	2	18
β-strand	397-398	2	19
β-strand	402	1	20
β-strand	406	1	20
β-strand	407-408	2	21
α-helix	417-420	4
β-strand	421-422	2	21
α-helix	424-436	13
β-strand	440-441	2	18
β-strand	453	1	22
β-strand	460	1	22
α-helix	462-468	7
β-strand	474-475	2	19
β-strand	480	1	23
α-helix	483-486	4
β-strand	489-491	3	19
β-strand	496-498	3	23
β-strand	500-505	6	24
α-helix	516-518	3
α-helix	524-544	21
α-helix	566-568	3
α-helix	573-584	12
α-helix	596-624	29
α-helix	637-640	4
β-strand	646-648	3	24
α-helix	649	1
β-strand	650	1	25
α-helix	654-661	8
α-helix	665-674	10
β-strand	683	1	25
α-helix	686-695	10
β-strand	700-705	6	24
α-helix	706-712	7
β-strand	720-723	4	24
β-strand	730-732	3	23
β-strand	735-737	3	19
α-helix	743-756	14
α-helix	758-763	6
α-helix	764-768	5
α-helix	785-786	2
β-strand	787	1	16
α-helix	788	1
α-helix	789-791	3
α-helix	793-819	27

Chain D: 27 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	395-399	5	26
β-strand	402	1	27
β-strand	406	1	27
β-strand	407-408	2	28
α-helix	412-414	3
α-helix	417-420	4
β-strand	421-422	2	28
α-helix	424-436	13
β-strand	440-444	5	26
α-helix	453-454	2
α-helix	462-468	7
β-strand	474-475	2	26
β-strand	480	1	29
α-helix	483-486	4
β-strand	489-491	3	26
α-helix	492	1
α-helix	494	1
β-strand	496-498	3	29
β-strand	500-505	6	30
α-helix	506-508	3
α-helix	516-518	3
β-strand	521	1	9
α-helix	523-543	21
α-helix	573-585	13
α-helix	596-613	18
α-helix	621-624	4
α-helix	638-640	3
β-strand	646-649	4	30
β-strand	650	1	31
α-helix	654-661	8
α-helix	665-674	10
β-strand	683	1	31
α-helix	686-695	10
β-strand	700-705	6	30
α-helix	706-712	7
β-strand	720-723	4	30
β-strand	730-732	3	29
β-strand	735-737	3	26
α-helix	743-756	14
α-helix	758-763	6
α-helix	764-768	5
α-helix	774-776	3
α-helix	778-780	3
α-helix	781-784	4
α-helix	789-791	3
α-helix	793-817	25

Chain E: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	8-27	20
β-strand	33-37	5	32
β-strand	56-60	5	32
β-strand	64-67	4	32
β-strand	76-78	3	32
α-helix	94-103	10
α-helix	105-122	18
α-helix	123-125	3
α-helix	132-158	27
β-strand	174-175	2	32
α-helix	177-205	29

Chain F: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-27	21
β-strand	33-37	5	33
β-strand	56-60	5	33
β-strand	64-67	4	33
β-strand	76-78	3	33
α-helix	95-103	9
α-helix	105-123	19
α-helix	133-158	26
β-strand	174-175	2	33
α-helix	177-206	30

Chain G: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	8-27	20
β-strand	33-37	5	34
β-strand	56-60	5	34
β-strand	64-67	4	34
β-strand	76-78	3	34
α-helix	94-103	10
α-helix	105-123	19
α-helix	133-158	26
β-strand	174-175	2	34
α-helix	177-205	29
α-helix	206-208	3

Chain H: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	8-27	20
β-strand	33-37	5	35
β-strand	56-60	5	35
β-strand	64-67	4	35
β-strand	76-78	3	35
α-helix	95-103	9
α-helix	105-123	19
α-helix	133-158	26
β-strand	174-175	2	35
α-helix	177-203	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform Flip of Glutamate receptor 2	A, B, C, D	protein	430	Rattus norvegicus	P19491 (AlphaFold model)
Voltage-dependent calcium channel gamma-2 subunit	E, F, G, H	protein	205	Mus musculus	O88602 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9DHR_1 Isoform Flip of Glutamate receptor 2 (chains A, B, C, D)
EQKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLAAEIAKHCGFKYKLTIVGDGKY
GARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKS
KPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHTEEFEDGRETQSSESTNE
FGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMV
SPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDKMWTYMRSAEPSVFVRTTAEGV
ARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDSKGYGIATPKGSSLGTPVNLAV
LKLSEQGVLDKLKNKWWYDKGECGAKDSGSKEKTSALSLSNVAGVFYILVGGLGLAMLVA
LIEFCYKSRA

Sequence of entity 2 (E, F, G, H), FASTA

>9DHR_2 Voltage-dependent calcium channel gamma-2 subunit (chains E, F, G, H)
RGVQMLLTTVGAFAAFSLMTIAVGTDYWLYSRGVCKTKSVSENETSKKNEEVMTHSGLWR
TCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGLCIAAS
EFYKTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGDPSKSDSKKNSYSYGWSFYFGAL
SFIIAEMVGVLAVHMFIDRHKQLTG

Ligands and cofactors

ID	Name	Formula	Copies
GLU	Glutamic acid	C5 H9 N O4	4

Primary citation

Glutamate gating of AMPA-subtype iGluRs at physiological temperatures. Kumar Mondal, A., Carrillo, E., Jayaraman, V. et al. Nature (2025) 641:788-796. DOI 10.1038/s41586-025-08770-0 · PubMed

Other PDB entries of the same protein (UniProt P19491 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6YK4 1.0 Å, Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the…
5NG9 1.15 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with agonist…
6YK5 1.15 Å, Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the…
6YK3 1.2 Å, Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the…
5JEI 1.23 Å, Crystal structure of the GluA2 LBD in complex with FW
4IGT 1.24 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the agonist…
4YU0 1.26 Å, Crystal structure of a tetramer of GluA2 TR mutant ligand binding domains bound with…
5NIH 1.3 Å, Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with agonist…
1MQI 1.35 Å, Crystal Structure of the GluR2 Ligand Binding Core (S1S2J) in Complex with…
5FTI 1.35 Å, Crystal structure of the GluA2 K738M-T744K LBD in complex with glutamate (lithium form)
4U21 1.39 Å, GluA2flip sLBD complexed with FW and (R,R)-2b crystal form E
4FAT 1.4 Å, Ligand-binding domain of GluA2 (flip) ionotropic glutamate receptor in complex with an…

Browse structure collections

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