9HPC: PDB entry 9HPC

The TMD and the LBD region of the AMPAR complex GluA3- TARP gamma2 in the apo state. Determined by electron microscopy at 2.59 Å resolution. Released 9 Jul 2025.

Method: Electron microscopy
Resolution: 2.59 Å
Organism: Rattus norvegicus
Chains: 8
Atoms: 17,952
Mol. weight: 1061.33 kDa
Released: 9 Jul 2025

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

Secondary structure: helices and β-sheets

9HPC contains 111 α-helices and 104 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: 22 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	398-401	4	1
β-strand	404	1	2
β-strand	408	1	2
β-strand	409-410	2	3
α-helix	414-416	3
α-helix	419-422	4
β-strand	423-424	2	3
α-helix	426-438	13
β-strand	443-446	4	1
β-strand	455	1	4
β-strand	462	1	4
α-helix	464-470	7
β-strand	476-477	2	1
β-strand	482	1	5
α-helix	485-488	4
β-strand	491-493	3	1
β-strand	498-500	3	5
β-strand	502-507	6	6
α-helix	508-511	4
α-helix	518-520	3
β-strand	523	1	7
α-helix	525-547	23
α-helix	550-553	4
α-helix	577-589	13
α-helix	600-632	33
α-helix	640-645	6
β-strand	650-652	3	6
β-strand	654	1	8
α-helix	658-665	8
α-helix	669-680	12
β-strand	687	1	8
α-helix	690-700	11
β-strand	704-709	6	6
α-helix	710-717	8
β-strand	724-727	4	6
β-strand	734-736	3	5
β-strand	739-741	3	1
α-helix	747-760	14
α-helix	762-768	7
α-helix	769-773	5
β-strand	791	1	9
α-helix	792	1
α-helix	793-796	4
α-helix	797-827	31

Chain B: 26 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	398-401	4	10
β-strand	409-410	2	11
α-helix	414-416	3
α-helix	419-422	4
β-strand	423-424	2	11
α-helix	426-438	13
β-strand	443-446	4	10
β-strand	455	1	12
β-strand	462	1	12
α-helix	464-470	7
β-strand	476-482	7	10
α-helix	485-488	4
β-strand	491-493	3	10
α-helix	494	1
α-helix	496	1
β-strand	498-500	3	10
β-strand	502-507	6	13
α-helix	508-509	2
α-helix	511-515	5
α-helix	518-520	3
β-strand	523	1	9
α-helix	525-547	23
α-helix	550-553	4
α-helix	577-589	13
α-helix	600-629	30
α-helix	640-645	6
β-strand	650-652	3	13
β-strand	654	1	14
α-helix	658-665	8
α-helix	669-680	12
β-strand	687	1	14
α-helix	690-699	10
β-strand	704-709	6	13
α-helix	710-717	8
β-strand	724-727	4	13
β-strand	734-741	8	10
α-helix	747-759	13
α-helix	762-768	7
α-helix	769-773	5
α-helix	790	1
β-strand	791	1	15
α-helix	792	1
α-helix	793-796	4
α-helix	797-827	31

Chain C: 22 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	398-401	4	16
β-strand	404	1	17
β-strand	408	1	17
β-strand	409-410	2	18
α-helix	419-422	4
β-strand	423-424	2	18
α-helix	426-438	13
β-strand	443-446	4	16
β-strand	455	1	19
β-strand	462	1	19
α-helix	464-470	7
β-strand	476-477	2	16
β-strand	482	1	20
α-helix	485-488	4
β-strand	491-493	3	16
β-strand	498-500	3	20
β-strand	502-507	6	21
α-helix	508-511	4
α-helix	518-520	3
β-strand	523	1	15
α-helix	525-547	23
α-helix	550-553	4
α-helix	577-588	12
α-helix	600-632	33
α-helix	640-645	6
β-strand	650-653	4	21
β-strand	654	1	22
α-helix	658-665	8
α-helix	669-680	12
β-strand	687	1	22
α-helix	690-699	10
β-strand	704-709	6	21
α-helix	710-717	8
β-strand	724-727	4	21
β-strand	734-736	3	20
β-strand	739-741	3	16
α-helix	747-760	14
α-helix	762-768	7
α-helix	769-773	5
α-helix	790	1
β-strand	791	1	23
α-helix	792	1
α-helix	793-796	4
α-helix	797-826	30

Chain D: 21 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	398-401	4	24
β-strand	404	1	25
β-strand	408	1	25
β-strand	409-410	2	26
α-helix	414-416	3
α-helix	419-422	4
β-strand	423-424	2	26
α-helix	426-438	13
β-strand	443-446	4	24
β-strand	455	1	27
β-strand	462	1	27
α-helix	464-470	7
β-strand	476-477	2	24
β-strand	482	1	28
α-helix	485-488	4
β-strand	491-493	3	24
β-strand	498-500	3	28
β-strand	502-507	6	29
α-helix	508-509	2
α-helix	511-515	5
α-helix	518-520	3
β-strand	523	1	23
α-helix	525-547	23
α-helix	577-588	12
α-helix	600-629	30
α-helix	640-645	6
β-strand	650-652	3	29
β-strand	654	1	30
α-helix	658-665	8
α-helix	669-679	11
β-strand	687	1	30
α-helix	690-699	10
β-strand	704-709	6	29
α-helix	710-717	8
β-strand	724-727	4	29
β-strand	734-736	3	28
β-strand	739-741	3	24
α-helix	747-759	13
α-helix	762-768	7
α-helix	769-773	5
β-strand	791	1	7
α-helix	793-796	4
α-helix	797-827	31

Chain W: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	34-38	5	31
β-strand	57-61	5	31
β-strand	65-68	4	31
β-strand	77-79	3	31
α-helix	95-104	10
α-helix	106-127	22
α-helix	133-161	29
β-strand	175-176	2	31
α-helix	178-209	32

Chain X: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	34-38	5	32
β-strand	57-61	5	32
β-strand	65-68	4	32
β-strand	77-79	3	32
α-helix	96-104	9
α-helix	106-127	22
α-helix	133-161	29
β-strand	175-176	2	32
α-helix	178-209	32

Chain Y: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	34-38	5	33
β-strand	57-61	5	33
β-strand	65-68	4	33
β-strand	77-79	3	33
α-helix	96-104	9
α-helix	106-127	22
α-helix	132-161	30
β-strand	175-176	2	33
α-helix	178-209	32

Chain Z: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	34-37	4	34
β-strand	58-61	4	34
β-strand	65-68	4	34
β-strand	77-79	3	34
α-helix	95-104	10
α-helix	106-127	22
α-helix	133-161	29
β-strand	175-176	2	34
α-helix	178-209	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit	A, B, C, D, W, X, Y, Z	protein	1179	Rattus norvegicus	P19492 (AlphaFold model), Q71RJ2 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, W, X, Y, Z), FASTA

>9HPC_1 Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit (chains A, B, C, D, W, X, Y, Z)
GDYKDDDDKFPNTISIGGLFMRNTVQEHSAFRFAVQLYNTNQNTTEKPFHLNYHVDHLDS
SNSFSVTNAFCSQFSRGVYAIFGFYDQMSMNTLTSFCGALHTSFVTPSFPTDADVQFVIQ
MRPALKGAILSLLSYYKWEKFVYLYDTERGFSVLQAIMEAAVQNNWQVTARSVGNIKDVQ
EFRRIIEEMDRRQEKRYLIDCEVERINTILEQVVILGKHSRGYHYMLANLGFTDILLERV
MHGGANITGFQIVNNENPMVQQFIQRWVRLDEREFPEAKNAPLKYTSALTHDAILVIAEA
FRYLRRQRVDVSRRGSAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRRTN
YTIDVYEMKVSGSRKAGYWNEYERFVPFSDQQISNDSSSSENRTIVVTTILESPYVMYKK
NHEQLEGNERYEGYCVDLAYEIAKHVGIKYKLSIVGDGKYGARDPETKIWNGMVGELVYG
RADIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIV
FAYIGVSVVLFLVSRFSPYEWHLEDNNEEPRDPQSPPDPPNEFGIFNSLWFSLGAFMQQG
CDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYG
TLDSGSTKEFFRRSKIAVYEKMWSYMKSAEPSVFTKTTADGVARVRKSKGKFAFLLESTM
NEYIEQRKPCDTMKVGGNLDSKGYGVATPKGSALGTPVNLAVLKLSEQGILDKLKNKWWY
DKGECGAKDSGSKDKTSALSLSNVAGVFYILVGGLGLAMMVALIEFCYKSRAESKRMKLT
KNTQNFKPAPAGGSGSGGLFDRGVQMLLTTVGAFAAFSLMTIAVGTDYWLYSRGVCKTKS
VSENETSKKNEEVMTHSGLWRTCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRAS
SIFPILSVILLFMGGLCIAASEFYKTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGDP
SKSDSKKNSYSYGWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLRATARATDYLQASAIT
RIPSYRYRYQRRSRSSSRSTEPSHSRDASPVGVKGFNTLPSTEISMYTLSRDPLKAATTP
TATYNSDRDNSFLQVHNCIQKDSKDSLHANTANRRTTPV

Primary citation

Architecture, dynamics and biogenesis of GluA3 AMPA glutamate receptors. Pokharna, A., Stockwell, I., Ivica, J. et al. Nature (2025) 645:535-543. DOI 10.1038/s41586-025-09325-z · PubMed

Other PDB entries of the same protein (UniProt P19492 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4F29 1.75 Å, Quisqualate bound to the ligand binding domain of GluA3i
3LSW 1.75 Å, Aniracetam bound to the ligand binding domain of GluA3
4F1Y 1.79 Å, CNQX bound to the ligand binding domain of GluA3
3M3K 1.79 Å, Ligand binding domain (S1S2) of GluA3 (flop)
4F3B 1.82 Å, Glutamate bound to the D655A mutant of the ligand binding domain of GluA3
4F39 1.83 Å, Kainate bound to the ligand binding domain of GluA3
3DLN 1.91 Å, Crystal structure of the binding domain of the AMPA subunit GluR3 bound to glutamate
4F2O 1.91 Å, Quisqualate bound to the D655A mutant of the ligand binding domain of GluA3
6FPJ 1.96 Å, Structure of the AMPAR GluA3 N-terminal domain bound to phosphate
3LSX 2.01 Å, Piracetam bound to the ligand binding domain of GluA3
4F22 2.06 Å, Kainate bound to the K660A mutant of the ligand binding domain of GluA3
4F3G 2.06 Å, Kainate bound to the ligand binding domain of GluA3i

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