9NR6: Noelin 1 with cerebellar GluA1/A4-ATD

The structure of Noelin 1 with cerebellar GluA1/A4-ATD. Determined by electron microscopy at 3.26 Å resolution. Released 2 Jul 2025.

Method: Electron microscopy
Resolution: 3.26 Å
Organisms: Rattus norvegicus, Mus musculus
Chains: 8
Atoms: 19,239
Mol. weight: 298.13 kDa
Ligands: CA, NAG
Released: 2 Jul 2025

Explore 9NR6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9NR6 contains 58 α-helices and 164 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: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	1
α-helix	19-30	12
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	112-122	11
β-strand	126-131	6	2
α-helix	138-150	13
β-strand	153-158	6	2
α-helix	164-174	11
β-strand	180-185	6	2
α-helix	191-195	5
α-helix	196-200	5
β-strand	208-212	5	2
α-helix	223-227	5
β-strand	231-236	6	2
α-helix	243-253	11
α-helix	258-259	2
α-helix	270-291	22
α-helix	315-324	10
β-strand	327-330	4	3
β-strand	333-336	4	3
β-strand	337	1	4
β-strand	342	1	1
β-strand	343	1	4
β-strand	347-353	7	2
β-strand	359-365	7	2
β-strand	369-372	4	2

Chain B: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	5
α-helix	18-32	15
β-strand	43-50	8	5
α-helix	58-68	11
β-strand	73-76	4	5
α-helix	83-92	10
β-strand	96-99	4	5
β-strand	111-113	3	5
α-helix	116-117	2
α-helix	120-128	9
β-strand	133-138	6	6
α-helix	145-157	13
β-strand	160-165	6	6
α-helix	171-183	13
β-strand	188-192	5	6
α-helix	195-208	14
β-strand	212	1	7
β-strand	216-219	4	6
α-helix	230-235	6
β-strand	236	1	7
β-strand	238-243	6	6
α-helix	250-260	11
α-helix	276-297	22
α-helix	322-330	9
β-strand	333-336	4	8
β-strand	339-342	4	8
β-strand	343	1	9
β-strand	349	1	9
β-strand	353-359	7	6
β-strand	364-371	8	6
β-strand	375-378	4	6

Chain C: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	10
α-helix	19-30	12
β-strand	36-43	8	10
α-helix	49-62	14
β-strand	66-69	4	10
α-helix	76-86	11
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	164-176	13
β-strand	181-185	5	11
α-helix	188-200	13
β-strand	209-212	4	11
β-strand	232-236	5	11
α-helix	243-253	11
α-helix	258-259	2
α-helix	270-291	22
α-helix	311-313	3
α-helix	315-324	10
β-strand	327-329	3	12
β-strand	334-336	3	12
β-strand	337	1	13
β-strand	342	1	10
β-strand	343	1	13
β-strand	347-353	7	11
β-strand	359-365	7	11
β-strand	370-372	3	11

Chain D: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	14
α-helix	18-32	15
β-strand	43-50	8	14
α-helix	56-68	13
β-strand	73-76	4	14
α-helix	83-92	10
β-strand	96-99	4	14
β-strand	111-113	3	14
α-helix	116-117	2
α-helix	119-128	10
β-strand	133-138	6	15
α-helix	145-157	13
β-strand	160-165	6	15
α-helix	171-183	13
β-strand	188-192	5	15
α-helix	195-208	14
β-strand	212	1	16
β-strand	216-219	4	15
α-helix	231-235	5
β-strand	236	1	16
β-strand	238-243	6	15
α-helix	250-260	11
α-helix	276-297	22
α-helix	322-330	9
β-strand	333-336	4	17
β-strand	339-342	4	17
β-strand	343	1	18
β-strand	349	1	18
β-strand	353-359	7	15
β-strand	364-371	8	15
β-strand	375-378	4	15

Chain E: 0 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	19
β-strand	21-25	5	19
β-strand	35-39	5	20
β-strand	45-50	6	20
β-strand	68-73	6	19
β-strand	78-83	6	19
β-strand	93-97	5	20
β-strand	108	1	21
β-strand	109	1	20
β-strand	113	1	20
β-strand	138-141	4	22
β-strand	144-147	4	21
β-strand	153	1	23
β-strand	156-159	4	22
β-strand	171-177	7	21
β-strand	180-187	8	21
β-strand	191-192	2	21
β-strand	209-210	2	22
β-strand	213	1	23
β-strand	223-228	6	21
β-strand	240-244	5	21

Chain F: 0 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	24
β-strand	21-25	5	24
β-strand	35-39	5	25
β-strand	45-50	6	25
β-strand	68-73	6	24
β-strand	78-83	6	24
β-strand	93-97	5	25
β-strand	108	1	26
β-strand	109	1	25
β-strand	113	1	25
β-strand	138-141	4	27
β-strand	144-147	4	26
β-strand	153	1	28
β-strand	156-159	4	27
β-strand	171-176	6	26
β-strand	183-187	5	26
β-strand	191-192	2	26
β-strand	209-210	2	27
β-strand	213	1	28
β-strand	223-228	6	26
β-strand	240-244	5	26

Chain G: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
α-helix	205-224	20
β-strand	229-233	5	29
β-strand	237-241	5	30
β-strand	247-251	5	31
α-helix	261	1
β-strand	262-266	5	31
β-strand	273-277	5	31
α-helix	281-284	4
β-strand	290-293	4	31
β-strand	298	1	32
β-strand	304-306	3	33
β-strand	309-313	5	33
β-strand	314	1	32
β-strand	319-324	6	33
β-strand	330-335	6	33
β-strand	356-360	5	34
β-strand	363-369	7	34
β-strand	376-382	7	34
β-strand	389-398	10	34
β-strand	405-408	4	35
β-strand	411-415	5	35
β-strand	423	1	36
β-strand	424-429	6	35
β-strand	434-437	4	35
β-strand	441	1	36
β-strand	449-455	7	30
α-helix	456-458	3
β-strand	460-465	6	30
β-strand	468-473	6	30
β-strand	474-479	6	29

Chain H: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	205-224	20
β-strand	229-233	5	29
β-strand	237-241	5	37
β-strand	247-250	4	38
β-strand	263-266	4	38
β-strand	273-275	3	38
α-helix	281-284	4
β-strand	291-293	3	38
β-strand	304-306	3	39
β-strand	309-313	5	39
β-strand	319-324	6	39
β-strand	330-335	6	39
β-strand	356-360	5	40
β-strand	363-369	7	40
β-strand	376-382	7	40
β-strand	389-398	10	40
β-strand	405-407	3	41
β-strand	411-415	5	41
β-strand	423-429	7	41
β-strand	434-441	8	41
β-strand	449-455	7	37
β-strand	460-465	6	37
β-strand	468-473	6	37
β-strand	474-479	6	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
Noelin	G, H	protein	277	Rattus norvegicus	Q62609 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9NR6_1 Glutamate receptor 1 (chains A, C)
ANFPNNIQIGGLFPNQQSQEHAAFRFALSQLTEPPKLLPQIDIVNISDSFEMTYRFCSQF
SKGVYAIFGFYERRTVNMLTSFCGALHVCFITPSFPVDTSNQFVLQLRPELQEALISIID
HYKWQTFVYIYDADRGLSVLQRVLDTAAEKNWQVTAVNILTTTEEGYRMLFQDLEKKKER
LVVVDCESERLNAILGQIVKLEKNGIGYHYILANLGFMDIDLNKFKESGANVTGFQLVNY
TDTIPARIMQQWRTSDSRDHTRVDWKRPKYTSALTYDGVKVMAEAFQSLRRQRIDISRRG
NAGDCLANPAVPWGQGIDIQRALQQVRFEGLTGNVQFNEKGRRTNYTLHVIEMKHDGIRK
IGYWNEDDKFVPA

Sequence of entity 2 (B, D), FASTA

>9NR6_2 Glutamate receptor 4 (chains B, D)
AFPSSVQIGGLFIRNTDQEYTAFRLAIFLHNTSPNASEAPFNLVPHVDNIETANSFAVTN
AFCSQYSRGVFAIFGLYDKRSVHTLTSFCSALHISLITPSFPTEGESQFVLQLRPSLRGA
LLSLLDHYEWNCFVFLYDTDRGYSILQAIMEKAGQNGWHVSAICVENFNDVSYRQLLEEL
DRRQEKKFVIDCEIERLQNILEQIVSVGKHVKGYHYIIANLGFKDISLERFIHGGANVTG
FQLVDFNTPMVTKLMDRWKKLDQREYPGSETPPKYTSALTYDGVLVMAETFRSLRRQKID
ISRRGNAGDCLANPAAPWGQGIDMERTLKQVRIQGLTGNVQFDHYGRRVNYTMDVFELKS
TGPRKVGYWNDMDKLVLI

Sequence of entity 3 (E, F), FASTA

>9NR6_3 11B8 scFv (chains E, F)
EVKLLESGGGLVQPGGSLKLSCAASGFDFSEYWMSWVRQAPGKGLEWIGEINPDSSSIDY
TPSLKDKIIISRDNAKKTLYLQLSKVRSEDTALYYCARPRGNYVVMDYWGQGTSVTVSSS
GGGGSGGGGSGGGGNIVLTQSPASLAVSLGQRATISCRASESVDSYGSSFVHWYQQKPGQ
PPKLLIFLASKLESGVPARFSGSGSRTDFTLTIDPVEADDAATYYCQQTNEDPYTFGGGT
KLEIKRASNWSHPQFEK

Sequence of entity 4 (G, H), FASTA

>9NR6_4 Noelin (chains G, H)
YDELQSRVSNLEERLRACMQKLACGKLTGISDPVTVKTSGSRFGSWMTDPLAPEGDNRVW
YMDGYHNNRFVREYKSMVDFMNTDNFTSHRLPHPWSGTGQVVYNGSIYFNKFQSHIIIRF
DLKTETILKTRSLDYAGYNNMYHYAWGGHSDIDLMVDENGLWAVYATNQNAGNIVISKLD
PVSLQILQTWNTSYPKRSAGEAFIICGTLYVTNGYSGGTKVHYAYQTNASTYEYIDIPFQ
NKYSHISMLDYNPKDRALYAWNNGHQTLYNVTLFHVI

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Primary citation

Gating and noelin clustering of native Ca 2+ -permeable AMPA receptors. Fang, C., 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…
8AYM 3.3 Å, Resting state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-55511118
8AYO 3.3 Å, Open state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and ligand JNJ-61432059

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