9HPE: PDB entry 9HPE

The NTD dimer and the interfacing LBD region of the AMPAR complex GluA3- TARP gamma2 in the apo state. Determined by electron microscopy at 2.9 Å resolution. Released 9 Jul 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Rattus norvegicus
Chains: 2
Atoms: 7,084
Mol. weight: 266.22 kDa
Ligands: NAG
Released: 9 Jul 2025

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

Secondary structure: helices and β-sheets

9HPE contains 32 α-helices and 50 β-strands across 2 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 B: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	1
α-helix	17-31	15
β-strand	42-49	8	1
α-helix	55-67	13
β-strand	72-75	4	1
α-helix	82-92	11
β-strand	95-98	4	1
α-helix	101-103	3
β-strand	110-112	3	1
α-helix	118-128	11
β-strand	132-137	6	2
β-strand	140	1	3
β-strand	142	1	3
α-helix	144-156	13
β-strand	159-164	6	2
α-helix	171-183	13
β-strand	188-192	5	2
α-helix	195-207	13
β-strand	216-219	4	2
α-helix	230-233	4
β-strand	238-240	3	2
β-strand	241-243	3	4
α-helix	250-259	10
α-helix	277-298	22
α-helix	317	1
α-helix	322-331	10
β-strand	334-337	4	5
β-strand	340-343	4	5
β-strand	344	1	6
β-strand	350	1	6
β-strand	354-358	5	4
β-strand	367-372	6	4
β-strand	377-379	3	4

Chain C: 19 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	7
α-helix	17-31	15
β-strand	42-49	8	7
α-helix	55-68	14
β-strand	72-75	4	7
α-helix	82-91	10
β-strand	95-98	4	7
α-helix	101-103	3
β-strand	110-112	3	7
α-helix	115-116	2
α-helix	118-128	11
β-strand	132-137	6	8
α-helix	144-156	13
β-strand	159-164	6	8
α-helix	171-183	13
β-strand	188-192	5	8
α-helix	195-208	14
β-strand	216-219	4	8
α-helix	224-226	3
α-helix	230-234	5
β-strand	238-240	3	8
β-strand	241-243	3	9
α-helix	250-259	10
α-helix	277-298	22
α-helix	317	1
α-helix	323-331	9
β-strand	335-337	3	10
β-strand	340-342	3	10
β-strand	344	1	11
β-strand	350	1	11
β-strand	354-358	5	9
β-strand	367-372	6	9
β-strand	377-379	3	9
β-strand	396-401	6	12
β-strand	404	1	13
β-strand	408	1	13
β-strand	409-410	2	14
β-strand	423-424	2	14
α-helix	426-438	13
β-strand	441-446	6	12
β-strand	454-455	2	15
β-strand	462-463	2	15
α-helix	464-470	7
β-strand	476	1	12
β-strand	477	1	16
α-helix	485-488	4
β-strand	491-493	3	16
β-strand	739-741	3	16
α-helix	747-759	13

Molecules and chains

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

Sequence of entity 1 (B, C), FASTA

>9HPE_1 Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit (chains B, C)
GDYKDDDDKFPNTISIGGLFMRNTVQEHSAFRFAVQLYNTNQNTTEKPFHLNYHVDHLDS
SNSFSVTNAFCSQFSRGVYAIFGFYDQMSMNTLTSFCGALHTSFVTPSFPTDADVQFVIQ
MRPALKGAILSLLSYYKWEKFVYLYDTERGFSVLQAIMEAAVQNNWQVTARSVGNIKDVQ
EFRRIIEEMDRRQEKRYLIDCEVERINTILEQVVILGKHSRGYHYMLANLGFTDILLERV
MHGGANITGFQIVNNENPMVQQFIQRWVRLDEREFPEAKNAPLKYTSALTHDAILVIAEA
FRYLRRQRVDVSRRGSAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRRTN
YTIDVYEMKVSGSRKAGYWNEYERFVPFSDQQISNDSSSSENRTIVVTTILESPYVMYKK
NHEQLEGNERYEGYCVDLAYEIAKHVGIKYKLSIVGDGKYGARDPETKIWNGMVGELVYG
RADIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIV
FAYIGVSVVLFLVSRFSPYEWHLEDNNEEPRDPQSPPDPPNEFGIFNSLWFSLGAFMQQG
CDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVSPIESAEDLAKQTEIAYG
TLDSGSTKEFFRRSKIAVYEKMWSYMKSAEPSVFTKTTADGVARVRKSKGKFAFLLESTM
NEYIEQRKPCDTMKVGGNLDSKGYGVATPKGSALGTPVNLAVLKLSEQGILDKLKNKWWY
DKGECGAKDSGSKDKTSALSLSNVAGVFYILVGGLGLAMMVALIEFCYKSRAESKRMKLT
KNTQNFKPAPAGGSGSGGLFDRGVQMLLTTVGAFAAFSLMTIAVGTDYWLYSRGVCKTKS
VSENETSKKNEEVMTHSGLWRTCCLEGNFKGLCKQIDHFPEDADYEADTAEYFLRAVRAS
SIFPILSVILLFMGGLCIAASEFYKTRHNIILSAGIFFVSAGLSNIIGIIVYISANAGDP
SKSDSKKNSYSYGWSFYFGALSFIIAEMVGVLAVHMFIDRHKQLRATARATDYLQASAIT
RIPSYRYRYQRRSRSSSRSTEPSHSRDASPVGVKGFNTLPSTEISMYTLSRDPLKAATTP
TATYNSDRDNSFLQVHNCIQKDSKDSLHANTANRRTTPV

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

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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