9NR8: Cerebellar GluA1/A4 ATD

The structure of cerebellar GluA1/A4 ATD. Determined by electron microscopy at 3.53 Å resolution. Released 2 Jul 2025.

Method: Electron microscopy
Resolution: 3.53 Å
Organisms: Rattus norvegicus, Mus musculus
Chains: 6
Atoms: 14,576
Mol. weight: 231.72 kDa
Ligands: NAG
Released: 2 Jul 2025

Explore 9NR8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9NR8 contains 59 α-helices and 120 β-strands across 6 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: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	1
α-helix	19-29	11
β-strand	36-43	8	1
α-helix	49-62	14
β-strand	66-69	4	1
α-helix	76-86	11
β-strand	89-92	4	1
β-strand	104-106	3	1
α-helix	109-110	2
α-helix	114-121	8
β-strand	126-131	6	2
α-helix	133-135	3
α-helix	138-150	13
β-strand	153-158	6	2
α-helix	164-174	11
β-strand	181-185	5	2
α-helix	188-200	13
β-strand	209-212	4	2
α-helix	224-226	3
β-strand	232-236	5	2
α-helix	243-253	11
α-helix	258-259	2
α-helix	270-291	22
α-helix	316-322	7
β-strand	329	1	3
β-strand	334	1	3
β-strand	336-337	2	4
β-strand	342	1	1
β-strand	343-344	2	4
β-strand	348-353	6	2
β-strand	360-365	6	2
β-strand	369-372	4	2

Chain B: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	5
β-strand	10-13	4	6
α-helix	18-32	15
β-strand	43	1	5
β-strand	48-50	3	6
α-helix	56-69	14
β-strand	73-75	3	6
α-helix	80-82	3
α-helix	83-92	10
β-strand	96-99	4	6
β-strand	111-113	3	6
α-helix	116-117	2
α-helix	119-128	10
β-strand	133-138	6	7
α-helix	145-157	13
β-strand	160-165	6	7
α-helix	171-183	13
β-strand	188-192	5	7
α-helix	195-208	14
β-strand	216-219	4	7
α-helix	231-235	5
β-strand	238-243	6	7
α-helix	250-260	11
α-helix	276-297	22
α-helix	322-329	8
β-strand	334-336	3	8
β-strand	339-341	3	8
β-strand	342-343	2	9
β-strand	349-350	2	9
β-strand	353-359	7	7
β-strand	365-371	7	7
β-strand	376-378	3	7

Chain C: 14 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	10
α-helix	19-29	11
β-strand	36-43	8	10
α-helix	49-62	14
β-strand	66-69	4	10
α-helix	76-85	10
β-strand	89-92	4	10
β-strand	104-106	3	10
α-helix	109-110	2
α-helix	114-121	8
β-strand	126-131	6	11
α-helix	133-135	3
α-helix	138-150	13
β-strand	153-158	6	11
α-helix	164-175	12
β-strand	181-185	5	11
α-helix	188-201	14
β-strand	205	1	12
β-strand	209-212	4	11
α-helix	224-226	3
β-strand	229	1	12
β-strand	232-236	5	11
α-helix	243-254	12
α-helix	270-291	22
α-helix	311-313	3
α-helix	316-323	8
β-strand	329-330	2	13
β-strand	333-334	2	13
β-strand	336-337	2	14
β-strand	342	1	10
β-strand	343-344	2	14
β-strand	347-353	7	11
β-strand	360-365	6	11
β-strand	369-372	4	11

Chain D: 15 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	15
β-strand	10-11	2	16
β-strand	13	1	17
α-helix	18-32	15
α-helix	37-39	3
β-strand	43-44	2	15
β-strand	47	1	16
β-strand	50	1	17
α-helix	56-69	14
β-strand	73-75	3	16
α-helix	80-82	3
α-helix	83-90	8
β-strand	96-99	4	16
β-strand	111-113	3	16
α-helix	116-117	2
α-helix	119-128	10
β-strand	133-138	6	18
α-helix	145-157	13
β-strand	160-165	6	18
α-helix	171-183	13
β-strand	188-192	5	18
α-helix	195-208	14
β-strand	216-219	4	18
α-helix	231-235	5
β-strand	238-243	6	18
α-helix	250-261	12
α-helix	273-274	2
α-helix	276-297	22
α-helix	322-329	8
β-strand	334-336	3	19
β-strand	339-341	3	19
β-strand	343	1	20
β-strand	349	1	20
β-strand	354-360	7	18
β-strand	363-370	8	18
β-strand	376-378	3	18

Chain E: 1 helix, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	21
β-strand	20-25	6	21
β-strand	35-39	5	22
β-strand	45-50	6	22
β-strand	68-73	6	21
β-strand	78-83	6	21
β-strand	93-97	5	22
β-strand	109	1	22
β-strand	113	1	22
β-strand	138-141	4	23
β-strand	144-147	4	24
β-strand	153-159	7	23
β-strand	164	1	25
β-strand	169	1	25
β-strand	171-176	6	24
β-strand	183-187	5	24
β-strand	191-192	2	24
β-strand	202	1	23
β-strand	208-213	6	23
α-helix	218-220	3
β-strand	222-228	7	24
β-strand	240-244	5	24

Chain F: 2 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	26
α-helix	16-18	3
β-strand	20-25	6	26
β-strand	35-39	5	27
β-strand	45-50	6	27
β-strand	68-73	6	26
β-strand	78-83	6	26
β-strand	93-97	5	27
β-strand	109	1	27
β-strand	113	1	27
β-strand	138-141	4	28
β-strand	144-147	4	29
β-strand	153-159	7	28
β-strand	164	1	30
β-strand	169	1	30
β-strand	171-176	6	29
β-strand	183-187	5	29
β-strand	191-192	2	29
β-strand	202	1	28
β-strand	209-213	5	28
α-helix	218-220	3
β-strand	223-228	6	29
β-strand	240-244	5	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor 1	A, C	protein	373	Rattus norvegicus	P19490 (AlphaFold model)
Glutamate receptor 4	B, D	protein	378	Rattus norvegicus	P19493 (AlphaFold model)
11B8 scFv	E, F	protein	257	Mus musculus

Sequence of entity 1 (A, C), FASTA

>9NR8_1 Glutamate receptor 1 (chains A, C)
ANFPNNIQIGGLFPNQQSQEHAAFRFALSQLTEPPKLLPQIDIVNISDSFEMTYRFCSQF
SKGVYAIFGFYERRTVNMLTSFCGALHVCFITPSFPVDTSNQFVLQLRPELQEALISIID
HYKWQTFVYIYDADRGLSVLQRVLDTAAEKNWQVTAVNILTTTEEGYRMLFQDLEKKKER
LVVVDCESERLNAILGQIVKLEKNGIGYHYILANLGFMDIDLNKFKESGANVTGFQLVNY
TDTIPARIMQQWRTSDSRDHTRVDWKRPKYTSALTYDGVKVMAEAFQSLRRQRIDISRRG
NAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRTNYTLHVIEMKHDGIRK
IGYWNEDDKFVPA

Sequence of entity 2 (B, D), FASTA

>9NR8_2 Glutamate receptor 4 (chains B, D)
AFPSSVQIGGLFIRNTDQEYTAFRLAIFLHNTSPNASEAPFNLVPHVDNIETANSFAVTN
AFCSQYSRGVFAIFGLYDKRSVHTLTSFCSALHISLITPSFPTEGESQFVLQLRPSLRGA
LLSLLDHYEWNCFVFLYDTDRGYSILQAIMEKAGQNGWHVSAICVENFNDVSYRQLLEEL
DRRQEKKFVIDCEIERLQNILEQIVSVGKHVKGYHYIIANLGFKDISLERFIHGGANVTG
FQLVDFNTPMVTKLMDRWKKLDQREYPGSETPPKYTSALTYDGVLVMAETFRSLRRQKID
ISRRGNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGNVQFDHYGRRVNYTMDVFELKS
TGPRKVGYWNDMDKLVLI

Sequence of entity 3 (E, F), FASTA

>9NR8_3 11B8 scFv (chains E, F)
EVKLLESGGGLVQPGGSLKLSCAASGFDFSEYWMSWVRQAPGKGLEWIGEINPDSSSIDY
TPSLKDKIIISRDNAKKTLYLQLSKVRSEDTALYYCARPRGNYVVMDYWGQGTSVTVSSS
GGGGSGGGGSGGGGNIVLTQSPASLAVSLGQRATISCRASESVDSYGSSFVHWYQQKPGQ
PPKLLIFLASKLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQTNEDPYTFGGGT
KLEIKRASNWSHPQFEK

Ligands and cofactors

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

Primary citation

Gating and noelin clustering of native Ca 2+ -permeable AMPA receptors. Fang, C.L., Spangler, C.J., Park, J. et al. Nature (2025) 645:526-534. DOI 10.1038/s41586-025-09289-0 · PubMed

Other PDB entries of the same protein (UniProt P19490 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2AWW 2.21 Å, Synapse associated protein 97 PDZ2 domain variant C378G with C-terminal GluR-A peptide
3SAJ 2.5 Å, Crystal Structure of glutamate receptor GluA1 Amino Terminal Domain
8C2H 2.64 Å, Transmembrane domain of active state homomeric GluA1 AMPA receptor in tandem with TARP…
8C2I 2.7 Å, Transmembrane domain of resting state homomeric GluA1 AMPA receptor in complex with TARP…
8AYN 2.8 Å, Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand LY3130481
8C1Q 2.82 Å, Resting state homomeric GluA1 AMPA receptor in complex with TARP gamma 3
8C1P 2.9 Å, Active state homomeric GluA1 AMPA receptor in complex with TARP gamma 3
7OCE 3.1 Å, Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and CNIH2 (LBD-TMD)
8AYL 3.2 Å, Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-61432059
9OVU 3.2 Å, Composite map of GluA1/A2 in the activated state, in complex with positive allosteric…
9NR6 3.26 Å, The structure of Noelin 1 with cerebellar GluA1/A4-ATD
8AYM 3.3 Å, Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-55511118

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