9HPK: PDB entry 9HPK

Open state TMD-LBD of the GluA3(R439G) with TARP gamma2. 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: 17,705
Mol. weight: 1062.13 kDa
Released: 9 Jul 2025

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

Secondary structure: helices and β-sheets

9HPK contains 105 α-helices and 101 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: 20 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	397-401	5	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	442-446	5	1
β-strand	455	1	4
β-strand	462	1	4
α-helix	464-470	7
β-strand	476-482	7	1
α-helix	485-488	4
β-strand	491-492	2	5
β-strand	498-500	3	1
β-strand	502-507	6	6
α-helix	518-520	3
β-strand	523	1	7
α-helix	525-547	23
α-helix	577-588	12
α-helix	600-627	28
α-helix	640-644	5
β-strand	650-653	4	6
β-strand	654	1	8
α-helix	658-665	8
α-helix	669-680	12
β-strand	687	1	8
α-helix	690-699	10
β-strand	704-709	6	6
α-helix	710-716	7
β-strand	724-725	2	6
β-strand	734-739	6	1
β-strand	740-741	2	5
α-helix	747-759	13
α-helix	762-767	6
α-helix	768-772	5
α-helix	790	1
β-strand	791	1	9
α-helix	792	1
α-helix	793-827	35

Chain B: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	397-401	5	10
β-strand	409-410	2	11
β-strand	423-424	2	11
α-helix	426-437	12
β-strand	442-446	5	10
α-helix	464-470	7
β-strand	476-477	2	10
α-helix	481	1
β-strand	482	1	12
α-helix	483	1
α-helix	485-488	4
β-strand	491-493	3	10
β-strand	498-500	3	12
β-strand	502-507	6	13
α-helix	518-520	3
β-strand	523	1	14
α-helix	525-547	23
α-helix	550-552	3
α-helix	577-588	12
α-helix	600-620	21
α-helix	621-623	3
α-helix	624-629	6
α-helix	640-645	6
β-strand	650-652	3	13
β-strand	654	1	15
α-helix	658-665	8
α-helix	669-679	11
β-strand	687	1	15
α-helix	690-699	10
β-strand	704-709	6	13
α-helix	710-717	8
β-strand	724-727	4	13
β-strand	734-736	3	12
β-strand	739-741	3	10
α-helix	747-759	13
α-helix	762-767	6
α-helix	768-772	5
β-strand	791	1	7
α-helix	797-827	31

Chain C: 21 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	396-401	6	16
β-strand	404	1	17
β-strand	408	1	17
β-strand	409-410	2	18
α-helix	414-416	3
α-helix	419-422	4
β-strand	423-424	2	18
α-helix	426-437	12
β-strand	441-446	6	16
β-strand	455	1	19
β-strand	462	1	19
α-helix	464-470	7
β-strand	476	1	16
β-strand	477-482	6	20
α-helix	485-488	4
β-strand	491-493	3	20
β-strand	498-500	3	20
β-strand	502-507	6	21
α-helix	518-520	3
β-strand	523	1	22
α-helix	525-547	23
α-helix	577-588	12
α-helix	600-627	28
α-helix	640-645	6
β-strand	650-652	3	21
β-strand	654	1	23
α-helix	658-665	8
α-helix	669-679	11
β-strand	687	1	23
α-helix	690-699	10
β-strand	704-709	6	21
α-helix	710-717	8
β-strand	724-727	4	21
β-strand	734-741	8	20
α-helix	747-760	14
α-helix	762-767	6
α-helix	768-772	5
α-helix	790	1
β-strand	791	1	14
α-helix	792	1
α-helix	793-796	4
α-helix	797-827	31

Chain D: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	397-401	5	24
β-strand	404	1	25
β-strand	408	1	25
β-strand	409-410	2	26
α-helix	414-416	3
α-helix	419-421	3
β-strand	423-424	2	26
α-helix	426-437	12
β-strand	442-446	5	24
β-strand	455	1	27
β-strand	462	1	27
α-helix	464-470	7
β-strand	476-482	7	24
α-helix	483	1
α-helix	485-488	4
β-strand	491-493	3	24
β-strand	498-500	3	24
β-strand	502-507	6	28
α-helix	518-520	3
β-strand	523	1	9
α-helix	525-547	23
α-helix	550-552	3
α-helix	577-588	12
α-helix	600-620	21
α-helix	624-629	6
α-helix	640-645	6
β-strand	650-652	3	28
β-strand	653-654	2	29
α-helix	658-664	7
α-helix	669-680	12
β-strand	686-687	2	29
α-helix	690-699	10
β-strand	704-709	6	28
α-helix	710-717	8
β-strand	724-727	4	28
β-strand	734-741	8	24
α-helix	747-760	14
α-helix	762-767	6
α-helix	768-772	5
β-strand	791	1	22
α-helix	793-795	3
α-helix	797-827	31

Chain W: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	34-38	5	30
β-strand	57-61	5	30
β-strand	65-68	4	30
β-strand	77-79	3	30
α-helix	80	1
α-helix	95-104	10
α-helix	106-127	22
α-helix	133-160	28
β-strand	175-176	2	30
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	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	133-160	28
β-strand	175-176	2	31
α-helix	178-207	30

Chain Y: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	34-36	3	32
β-strand	59-61	3	32
β-strand	65-68	4	32
β-strand	74	1	32
β-strand	77-79	3	32
α-helix	95-104	10
α-helix	106-127	22
α-helix	133-160	28
β-strand	176	1	32
α-helix	178-209	32

Chain Z: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-29	23
β-strand	34-36	3	33
β-strand	59-61	3	33
β-strand	65-68	4	33
β-strand	77-79	3	33
α-helix	95-104	10
α-helix	106-127	22
α-helix	133-160	28
β-strand	175-176	2	33
α-helix	178-208	31

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

>9HPK_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
NHEQLEGNERYEGYCVDLAYEIAKHVRIKYKLSIVGDGKYGARDPETKIWNGMVGELVYG
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

Browse structure collections

About this viewer

MolViewer shows 9HPK directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.