9E9D: PDB entry 9E9D

Structure of full length AMPA receptor GluA2 and auxiliary subunit TARP gamma-2 in complex with anti-miR 17 oligonucleotide RGLS4326. Determined by electron microscopy at 3.24 Å resolution. Released 11 Feb 2026.

Method: Electron microscopy
Resolution: 3.24 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 30,792
Mol. weight: 463.6 kDa
Ligands: A1BX3
Released: 11 Feb 2026

Explore 9E9D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E9D contains 142 α-helices and 190 β-strands across 4 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: 34 helices, 45 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	1
α-helix	23-35	13
β-strand	44-49	6	1
α-helix	55-66	12
β-strand	73-75	3	1
α-helix	82-92	11
β-strand	96-98	3	1
α-helix	101-103	3
β-strand	111-112	2	1
α-helix	115-116	2
α-helix	118-128	11
α-helix	148-155	8
α-helix	173-180	8
β-strand	191-192	2	2
α-helix	198-211	14
β-strand	219-220	2	2
β-strand	241	1	2
β-strand	243-244	2	3
α-helix	253-264	12
α-helix	280-300	21
α-helix	320-321	2
α-helix	326-333	8
β-strand	339-340	2	4
β-strand	343-344	2	4
β-strand	358	1	5
β-strand	361-362	2	3
β-strand	363-364	2	6
β-strand	367-368	2	6
β-strand	372-373	2	7
β-strand	374	1	5
β-strand	381-382	2	7
β-strand	394-395	2	8
β-strand	397-399	3	9
β-strand	407-408	2	10
α-helix	417-420	4
β-strand	421-422	2	10
α-helix	424-436	13
β-strand	439-440	2	8
β-strand	443-444	2	9
β-strand	474-480	7	9
α-helix	483-486	4
β-strand	490	1	11
β-strand	496	1	9
β-strand	500	1	12
β-strand	502-504	3	13
β-strand	521	1	14
α-helix	525-542	18
α-helix	548-550	3
β-strand	551	1	15
β-strand	567	1	15
α-helix	605-611	7
α-helix	614-619	6
β-strand	646-648	3	13
β-strand	650	1	16
α-helix	656-661	6
α-helix	665-675	11
β-strand	683	1	16
α-helix	686-689	4
α-helix	691-694	4
β-strand	700-702	3	13
β-strand	705	1	12
β-strand	721-723	3	13
β-strand	732-735	4	9
β-strand	736	1	11
α-helix	745-748	4
α-helix	758-767	10
β-strand	787	1	17
α-helix	795-800	6
α-helix	803-818	16
α-helix	1005-1007	3
α-helix	1010-1028	19
β-strand	1033-1035	3	18
β-strand	1058-1060	3	18
β-strand	1066	1	19
β-strand	1076	1	19
α-helix	1092-1103	12
α-helix	1105-1123	19
α-helix	1131-1158	28
α-helix	1179-1204	26

Chains B and D: 37 helices, 50 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	20
β-strand	16-18	3	21
α-helix	23-35	13
β-strand	43	1	20
β-strand	48-49	2	21
α-helix	55-68	14
β-strand	74-75	2	21
α-helix	82-92	11
β-strand	97-98	2	21
α-helix	101-103	3
β-strand	111-112	2	21
α-helix	115-116	2
α-helix	118-127	10
β-strand	134	1	22
β-strand	137	1	23
α-helix	139-141	3
α-helix	146-156	11
β-strand	161	1	22
α-helix	173-187	15
β-strand	195	1	23
α-helix	198-209	12
β-strand	216	1	24
β-strand	218	1	24
β-strand	219-225	7	25
α-helix	234-236	3
β-strand	241-246	6	25
α-helix	253-263	11
α-helix	280-300	21
α-helix	324-333	10
β-strand	346	1	26
β-strand	352	1	21
β-strand	354	1	26
β-strand	358-363	6	25
β-strand	368-374	7	25
β-strand	380-381	2	25
β-strand	395-397	3	27
β-strand	407-408	2	28
α-helix	418-420	3
β-strand	421-422	2	28
α-helix	424-436	13
β-strand	440-442	3	27
β-strand	453	1	29
β-strand	460	1	29
β-strand	474	1	27
β-strand	475	1	30
β-strand	480	1	31
α-helix	483-486	4
β-strand	490-491	2	30
β-strand	496-497	2	31
β-strand	502-505	4	32
α-helix	506-507	2
α-helix	510-513	4
α-helix	516-518	3
β-strand	521	1	33
α-helix	523-543	21
α-helix	548-550	3
β-strand	551	1	34
β-strand	567	1	34
α-helix	604-611	8
α-helix	614-623	10
α-helix	636-640	5
β-strand	648	1	32
β-strand	650	1	35
α-helix	657-661	5
α-helix	666-675	10
β-strand	683	1	35
α-helix	686-695	10
β-strand	702-703	2	32
α-helix	709-712	4
β-strand	720-723	4	32
β-strand	731-732	2	31
β-strand	735-736	2	30
α-helix	743-756	14
α-helix	758-767	10
β-strand	787	1	14
α-helix	794-818	25
α-helix	1005-1027	23
β-strand	1033	1	36
β-strand	1037	1	37
β-strand	1056	1	37
β-strand	1058-1059	2	38
β-strand	1060	1	36
β-strand	1066-1067	2	38
α-helix	1093-1103	11
α-helix	1105-1126	22
α-helix	1132-1158	27
α-helix	1177-1208	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit	A, B, C, D	protein	1028	Rattus norvegicus	P19491 (AlphaFold model), Q71RJ2 (AlphaFold model)

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

>9E9D_1 Isoform Flip of Glutamate receptor 2,Voltage-dependent calcium channel gamma-2 subunit (chains A, B, C, D)
NSIQIGGLFPRGADQEYSAFRVGMVQFSTSEFRLTPHIDNLEVANSFAVTNAFCSQFSRG
VYAIFGFYDKKSVNTITSFCGTLHVSFITPSFPTDGTHPFVIQMRPDLKGALLSLIEYYQ
WDKFAYLYDSDRGLSTLQAVLDSAAEKKWQVTAINVGNINNDKKDETYRSLFQDLELKKE
RRVILDCERDKVNDIVDQVITIGKHVKGYHYIIANLGFTDGDLLKIQFGGAEVSGFQIVD
YDDSLVSKFIERWSTLEEKEYPGAHTATIKYTSALTYDAVQVMTEAFRNLRKQRIEISRR
GNAGDCLANPAVPWGQGVEIERALKQVQVEGLSGNIKFDQNGKRINYTINIMELKTNGPR
KIGYWSEVDKMVLTEDDTSGLEQKTVVVTTILESPYVMMKKNHEMLEGNERYEGYCVDLA
AEIAKHCGFKYKLTIVGDGKYGARDADTKIWNGMVGELVYGKADIAIAPLTITLVREEVI
DFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPY
EWHTEEFEDGRETQSSESTNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFT
LIIISSYTANLAAFLTVERMVSPIESAEDLSKQTEIAYGTLDSGSTKEFFRRSKIAVFDK
MWTYMRSAEPSVFVRTTAEGVARVRKSKGKYAYLLESTMNEYIEQRKPCDTMKVGGNLDS
KGYGIATPKGSSLGTPVNLAVLKLSEQGVLDKLKNKWWYDKGECGAKDSGSKEKTSALSL
SNVAGVFYILVGGLGLAMLVALIEFCYKSRAEAKRMKGTGLFDRGVQMLLTTVGAFAAFS
LMTIAVGTDYWLYSRGVCKTKSVSEDETSKKNEEVMTHSGLWRTCCLEGNFKGLCKQIDH
FPEDADYEADTAEYFLRAVRASSIFPILSVILLFMGGLCIAASEFYKTRHNIILSAGIFF
VSAGLSNIIGIIVYISANAGDPSKSDSKKNSYSYGWSFYFGALSFIIAEMVGVLAVHMFI
DRHKQLTG

Ligands and cofactors

ID	Name	Formula	Copies
A1BX3	O-{[(1S,3S,4R,6S,7R)-7-{[(R)-{[(1R,3R,4R,6S,7R)-3-(2-amino-6-oxo-1,6-dihydro-9H…	C33 H41 N9 O18 P2 S2	4

Primary citation

The nucleobase guanine at the 3'-terminus of oligonucleotide RGLS4326 drives off-target AMPAR inhibition and CNS toxicity. Valencia, T., Yen, L.Y., Berman, C. et al. Nat Commun (2025) 16:10762-10762. DOI 10.1038/s41467-025-65799-5 · 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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