9QDN: GluA4

GluA4 in complex with TARP-2, resting state I, structure of TMD/LBD. Determined by electron microscopy at 2.71 Å resolution. Released 24 Sept 2025.

Method: Electron microscopy
Resolution: 2.71 Å
Organism: Rattus norvegicus
Chains: 8
Atoms: 18,807
Mol. weight: 545.37 kDa
Ligands: E2Q, OLC, PLM
Released: 24 Sept 2025

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

Secondary structure: helices and β-sheets

9QDN contains 114 α-helices and 108 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.

Chains A and C: 22 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	420-421	2	10
β-strand	429-430	2	11
α-helix	434-436	3
α-helix	439-442	4
β-strand	443-444	2	11
α-helix	446-458	13
β-strand	465-466	2	10
β-strand	473-475	3	12
β-strand	482-484	3	12
α-helix	485-490	6
β-strand	497	1	13
β-strand	502	1	14
α-helix	505-508	4
β-strand	512-513	2	13
β-strand	518-520	3	14
β-strand	522	1	15
β-strand	524-527	4	16
α-helix	533-535	3
α-helix	538-540	3
β-strand	543	1	17
α-helix	545-567	23
α-helix	595-606	12
α-helix	618-651	34
α-helix	658-663	6
β-strand	668-670	3	16
β-strand	672	1	18
α-helix	676-683	8
α-helix	687-698	12
β-strand	705	1	18
α-helix	708-716	9
β-strand	722-724	3	16
β-strand	727	1	15
α-helix	728-734	7
β-strand	742-745	4	16
β-strand	752-754	3	14
β-strand	757-758	2	13
α-helix	765-777	13
α-helix	780-786	7
α-helix	787-791	5
α-helix	808	1
β-strand	809	1	7
α-helix	810	1
α-helix	811-813	3
α-helix	815-842	28

Chains B and D: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	417-419	3	32
β-strand	429	1	33
α-helix	440-442	3
β-strand	444	1	33
α-helix	446-456	11
β-strand	462-464	3	32
β-strand	474-476	3	34
β-strand	481-483	3	34
α-helix	485-490	6
β-strand	496	1	32
β-strand	497-502	6	35
α-helix	503	1
α-helix	507-509	3
β-strand	511-513	3	35
β-strand	518-520	3	35
β-strand	522-527	6	36
α-helix	528-529	2
α-helix	531-535	5
α-helix	538-540	3
β-strand	543	1	31
α-helix	545-567	23
α-helix	595-606	12
α-helix	618-647	30
α-helix	650-652	3
α-helix	658-663	6
β-strand	668-670	3	36
β-strand	672	1	37
α-helix	677-683	7
α-helix	687-697	11
β-strand	705	1	37
α-helix	708-717	10
β-strand	722-727	6	36
α-helix	728-731	4
α-helix	734-736	3
β-strand	742-745	4	36
β-strand	752-759	8	35
α-helix	765-778	14
α-helix	780-786	7
α-helix	787-791	5
α-helix	808	1
β-strand	809	1	17
α-helix	810	1
α-helix	815-842	28

Chains E and G: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	9-29	21
β-strand	34-35	2	21
β-strand	37-38	2	22
β-strand	57-58	2	22
β-strand	59-61	3	21
β-strand	65-68	4	21
β-strand	77-79	3	21
α-helix	80	1
α-helix	94-104	11
α-helix	106-127	22
α-helix	133-160	28
β-strand	175-176	2	21
α-helix	178-213	36

Chains F and H: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	8-29	22
β-strand	34-38	5	38
β-strand	57-61	5	38
β-strand	65-68	4	38
β-strand	74	1	38
β-strand	77-79	3	38
α-helix	93-104	12
α-helix	106-127	22
α-helix	133-159	27
β-strand	175-176	2	38
α-helix	178-211	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Voltage-dependent calcium channel gamma-2 subunit	E, F, G, H	protein	323	Rattus norvegicus	Q71RJ2 (AlphaFold model)
Isoform 2 of Glutamate receptor 4	A, B, C, D	protein	882	Rattus norvegicus	P19493 (AlphaFold model)

Sequence of entity 1 (E, F, G, H), FASTA

>9QDN_1 Voltage-dependent calcium channel gamma-2 subunit (chains E, F, G, H)
MGLFDRGVQMLLTIVGAFAAFSLMTIAVGTDYWLYSRGVCKTKSVSENETSKKNEEVMTH
SGLWRTCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGL
CIAASEFYKTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGDPSKSDSKKNSYSYGWSF
YFGALSFIIAEMVGVLAVHMFIDRHKQLRATARATDYLQASAITRIPSYRYRYQRRSRSS
SRSTEPSHSRDASPVGVKGFNTLPSTEISMYTLSRDPLKAATTPTATYNSDRDNSFLQVH
NCIQKDSKDSLHANTANRRTTPV

Sequence of entity 2 (A, B, C, D), FASTA

>9QDN_2 Isoform 2 of Glutamate receptor 4 (chains A, B, C, D)
GAFPSSVQIGGLFIRNTDQEYTAFRLAIFLHNTSPNASEAPFNLVPHVDNIETANSFAVT
NAFCSQYSRGVFAIFGLYDKRSVHTLTSFCSALHISLITPSFPTEGESQFVLQLRPSLRG
ALLSLLDHYEWNCFVFLYDTDRGYSILQAIMEKAGQNGWHVSAICVENFNDVSYRQLLEE
LDRRQEKKFVIDCEIERLQNILEQIVSVGKHVKGYHYIIANLGFKDISLERFIHGGANVT
GFQLVDFNTPMVTKLMDRWKKLDQREYPGSETPPKYTSALTYDGVLVMAETFRSLRRQKI
DISRRGNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGNVQFDHYGRRVNYTMDVFELK
STGPRKVGYWNDMDKLVLIQDMPTLGNDTAAIENRTVVVTTIMESPYVMYKKNHEMFEGN
DKYEGYCVDLASEIAKHIGIKYKIAIVPDGKYGARDADTKIWNGMVGELVYGKAEIAIAP
LTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSV
VLFLVSRFSPYEWHTEEPEDGKEGPSDQPPNEFGIFNSLWFSLGAFMQQGCDISPRSLSG
RIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYGTLDSGSTKEF
FRRSKIAVYEKMWTYMRSAEPSVFTRTTAEGVARVRKSKGKFAFLLESTMNEYIEQRKPC
DTMKVGGNLDSKGYGVATPKGSSLRTPVNLAVLKLSEAGVLDKLKNKWWYDKGECGPKDS
GSKDKTSALSLSNVAGVFYILVGGLGLAMLVALIEFCYKSRAEAKRMKLTFSEATRNKAR
LSITGSVGENGRVLTPDCPKAVHTGTAIRQSSGLAVIASDLP

Ligands and cofactors

ID	Name	Formula	Copies
E2Q	6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide	C12 H8 N4 O6 S	4
OLC	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate	C21 H40 O4	4
PLM	Palmitic acid	C16 H32 O2	16

Primary citation

GluA4 AMPA receptor gating mechanisms and modulation by auxiliary proteins. Vega-Gutierrez, C., Picanol-Parraga, J., Sanchez-Valls, I. et al. Nat Struct Mol Biol (2025) 32:2416-2428. DOI 10.1038/s41594-025-01666-7 · PubMed

Other PDB entries of the same protein (UniProt Q71RJ2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9HPC 2.59 Å, The TMD and the LBD region of the AMPAR complex GluA3- TARP gamma2 in the apo state.
9HPK 2.59 Å, Open state TMD-LBD of the GluA3(R439G) with TARP gamma2
9HPE 2.9 Å, The NTD dimer and the interfacing LBD region of the AMPAR complex GluA3- TARP gamma2 in…
9QFH 2.9 Å, The composite map of of the AMPAR complex GluA3- TARP gamma2 in the apo state.
9RMW 2.9 Å, GluA4 in complex with TARP-2, open state, structure of TMD/LBD domains
8P3Q 2.95 Å, Homomeric GluA2 flip R/G-unedited Q/R-edited F231A mutant in tandem with TARP gamma-2,…
8P3S 2.95 Å, Homomeric GluA2 flip R/G-unedited Q/R-edited F231A mutant in tandem with TARP gamma-2,…
8C1S 3.0 Å, Transmembrane domain of resting state homomeric GluA2 F231A mutant AMPA receptor in…
9RN7 3.1 Å, GluA4 in complex with TARP-2, Desensitized state, structure of TMD domain
9RNH 3.1 Å, GluA4 in complex with TARP-2, Resting II state, structure of TMD domain
8C1R 3.2 Å, Resting state homomeric GluA2 F231A mutant AMPA receptor in complex with TARP gamma-2
9E9D 3.24 Å, Structure of full length AMPA receptor GluA2 and auxiliary subunit TARP gamma-2 in…

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