9E9E: PDB entry 9E9E

Structure of AMPA receptor GluA2 and auxiliary subunit TARP gamma-2 (LBD-TMD) 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: 18,546
Mol. weight: 463.6 kDa
Ligands: A1BX3
Released: 11 Feb 2026

Explore 9E9E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9E9E contains 94 α-helices and 112 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: 24 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	395	1	1
β-strand	397-399	3	2
β-strand	407-408	2	3
α-helix	418-420	3
β-strand	421-422	2	3
α-helix	424-436	13
β-strand	440	1	1
β-strand	443-444	2	2
α-helix	463-469	7
β-strand	474-480	7	2
α-helix	483-486	4
β-strand	489-490	2	4
β-strand	496	1	2
β-strand	500-504	5	5
α-helix	516-518	3
β-strand	521	1	6
α-helix	523-544	22
α-helix	548-550	3
β-strand	551	1	7
β-strand	567	1	7
α-helix	573-584	12
α-helix	598-629	32
α-helix	636-641	6
β-strand	646-648	3	5
β-strand	650	1	8
α-helix	654-661	8
α-helix	665-675	11
β-strand	683	1	8
α-helix	686-695	10
β-strand	700-705	6	5
α-helix	706-713	8
β-strand	721-723	3	5
β-strand	732-735	4	2
β-strand	736-737	2	4
α-helix	743-755	13
α-helix	759-764	6
α-helix	765-769	5
β-strand	787	1	9
α-helix	794-819	26
α-helix	1006-1028	23
β-strand	1033	1	10
β-strand	1036	1	11
β-strand	1057	1	11
β-strand	1060	1	10
β-strand	1065	1	12
β-strand	1077	1	12
α-helix	1078-1079	2
α-helix	1092-1103	12
α-helix	1105-1126	22
α-helix	1132-1160	29
α-helix	1176-1206	31

Chains B and D: 23 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	395-397	3	13
β-strand	407-408	2	14
α-helix	417-419	3
β-strand	421-422	2	14
α-helix	424-436	13
β-strand	440-442	3	13
β-strand	450-454	5	15
β-strand	459-462	4	15
α-helix	463-469	7
β-strand	474	1	13
β-strand	475	1	16
β-strand	480	1	17
β-strand	489	1	18
β-strand	496-498	3	17
β-strand	500-505	6	19
α-helix	506-513	8
α-helix	516-518	3
β-strand	521	1	20
α-helix	523-544	22
α-helix	548-550	3
β-strand	551	1	21
β-strand	567	1	21
α-helix	576-582	7
α-helix	596-625	30
α-helix	636-641	6
β-strand	646-648	3	19
β-strand	650	1	22
α-helix	657-661	5
α-helix	666-674	9
β-strand	683	1	22
α-helix	686-695	10
β-strand	700-705	6	19
α-helix	706-713	8
β-strand	720-723	4	19
β-strand	730-732	3	17
β-strand	735	1	16
β-strand	737	1	18
α-helix	743-756	14
α-helix	758-763	6
α-helix	764-769	6
β-strand	787	1	6
α-helix	794-819	26
α-helix	1005-1028	24
β-strand	1036-1037	2	23
β-strand	1056-1057	2	23
β-strand	1058-1059	2	24
β-strand	1066-1067	2	24
β-strand	1076	1	24
α-helix	1093-1103	11
α-helix	1105-1126	22
α-helix	1132-1160	29
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

>9E9E_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

About this viewer

MolViewer shows 9E9E 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.