7SAA: Glutamate receptor ionotropic, NMDA 1

Glycine and glutamate bound GluN1a-GluN2B NMDA receptors in non-active 1 conformation at 2.97 Angstrom resolution. Determined by electron microscopy at 2.97 Å resolution. Released 20 Jul 2022.

Method: Electron microscopy
Resolution: 2.97 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 23,618
Mol. weight: 391.72 kDa
Ligands: GLU, GLY, NAG
Released: 20 Jul 2022

Explore 7SAA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SAA contains 138 α-helices and 156 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.

Chain A: 35 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	26	1	1
β-strand	29-32	4	2
α-helix	36-50	15
β-strand	59	1	1
β-strand	62-65	4	2
α-helix	71-85	15
β-strand	90-92	3	2
α-helix	105-113	9
β-strand	118-120	3	2
α-helix	127-129	3
β-strand	138-139	2	2
α-helix	144-146	3
α-helix	149-157	9
β-strand	163-168	6	3
α-helix	171-186	16
β-strand	193-197	5	3
α-helix	205-211	7
β-strand	216	1	4
β-strand	218-222	5	3
α-helix	225-237	13
β-strand	246-248	3	3
α-helix	256-260	5
β-strand	267-271	5	3
α-helix	277-295	19
α-helix	303-305	3
α-helix	314-315	2
α-helix	319-326	8
β-strand	330	1	5
β-strand	338	1	5
β-strand	340	1	6
β-strand	346	1	6
β-strand	351-357	7	3
β-strand	360-367	8	3
β-strand	372-374	3	3
β-strand	392	1	4
β-strand	397-402	6	7
β-strand	405	1	8
β-strand	409	1	8
β-strand	410-413	4	9
α-helix	414-415	2
α-helix	420-422	3
β-strand	424	1	10
α-helix	429	1
β-strand	430	1	10
α-helix	431-432	2
β-strand	434-439	6	9
β-strand	450-456	7	9
α-helix	458-470	13
β-strand	473-478	6	7
β-strand	487-488	2	11
β-strand	497-498	2	11
α-helix	500-506	7
β-strand	512-518	7	7
α-helix	519	1
α-helix	523-525	3
β-strand	528-529	2	7
β-strand	534	1	7
β-strand	538-543	6	12
α-helix	560-583	24
α-helix	603-615	13
α-helix	627-656	30
α-helix	670-673	4
β-strand	681-682	2	12
β-strand	684	1	13
α-helix	688-693	6
α-helix	697-699	3
α-helix	700-706	7
β-strand	711	1	13
α-helix	714-722	9
β-strand	728-732	5	12
α-helix	733-740	8
β-strand	746-753	8	12
β-strand	758-762	5	7
α-helix	769-781	13
α-helix	784-792	9
α-helix	811-825	15
α-helix	827-840	14

Chain B: 33 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	36-42	7	14
α-helix	47-54	8
β-strand	67-73	7	14
α-helix	78-91	14
β-strand	94-99	6	14
α-helix	107-118	12
β-strand	123-125	3	14
α-helix	128-131	4
β-strand	143-145	3	14
α-helix	150-163	14
β-strand	168-173	6	15
α-helix	179-191	13
β-strand	198-203	6	15
α-helix	213-220	8
β-strand	227-231	5	15
α-helix	234-247	14
β-strand	255-258	4	15
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	15
α-helix	289-311	23
α-helix	327-329	3
α-helix	333-338	6
β-strand	343-344	2	16
β-strand	347-348	2	16
β-strand	362-367	6	15
β-strand	373-380	8	15
β-strand	383-386	4	15
α-helix	391-393	3
β-strand	405-410	6	17
β-strand	413	1	18
β-strand	417	1	18
β-strand	418-421	4	17
β-strand	434-439	6	17
β-strand	452-458	7	17
α-helix	460-472	13
β-strand	475-480	6	17
β-strand	489-490	2	19
β-strand	493-494	2	19
α-helix	496-502	7
β-strand	508-509	2	17
α-helix	513	1
β-strand	514	1	20
α-helix	515	1
α-helix	518-521	4
β-strand	524-525	2	17
β-strand	530-532	3	20
β-strand	534-539	6	21
α-helix	540-541	2
α-helix	556-578	23
α-helix	603-613	11
α-helix	626-655	30
α-helix	669-672	4
β-strand	683-684	2	21
α-helix	690-698	9
α-helix	700-705	6
α-helix	706-709	4
α-helix	714-722	9
β-strand	728-732	5	21
α-helix	733-740	8
β-strand	748-750	3	21
α-helix	751-753	3
β-strand	760-762	3	20
β-strand	765-766	2	17
α-helix	772-786	15
α-helix	788-796	9
α-helix	815-844	30

Chain C: 37 helices, 43 β-strands

Element	Residues	Length	Sheet
β-strand	27-32	6	22
α-helix	36-49	14
β-strand	60-65	6	22
α-helix	71-85	15
β-strand	90-92	3	22
α-helix	105-112	8
β-strand	118-120	3	22
α-helix	126-129	4
β-strand	137-138	2	22
α-helix	144-146	3
α-helix	149-158	10
β-strand	163-168	6	23
α-helix	171-186	16
β-strand	193-197	5	23
α-helix	205-213	9
β-strand	216	1	24
β-strand	218-222	5	23
α-helix	228-235	8
β-strand	246-248	3	23
α-helix	258-261	4
α-helix	262-263	2
β-strand	267	1	23
β-strand	269-271	3	25
α-helix	277-295	19
α-helix	303-305	3
α-helix	319-325	7
β-strand	333	1	26
β-strand	336	1	26
β-strand	340	1	27
β-strand	346	1	27
β-strand	351-353	3	25
β-strand	365-368	4	25
β-strand	371-374	4	25
α-helix	382-384	3
α-helix	388-389	2
β-strand	392	1	24
β-strand	397-402	6	28
β-strand	405	1	29
β-strand	409	1	29
β-strand	410-413	4	28
α-helix	414-415	2
α-helix	420-422	3
β-strand	424	1	30
β-strand	430	1	30
α-helix	431-432	2
β-strand	434-439	6	28
α-helix	447-448	2
β-strand	450-456	7	28
α-helix	458-470	13
β-strand	473-478	6	28
β-strand	487-489	3	31
β-strand	496-498	3	31
α-helix	500-506	7
β-strand	512-513	2	28
β-strand	518	1	32
α-helix	521-524	4
β-strand	527-529	3	28
β-strand	534-535	2	32
β-strand	538-543	6	33
α-helix	544-549	6
α-helix	560-583	24
α-helix	605-614	10
α-helix	627-656	30
α-helix	670-673	4
β-strand	681-682	2	33
β-strand	684	1	34
α-helix	688-695	8
α-helix	697-699	3
α-helix	700-707	8
β-strand	711	1	34
α-helix	714-722	9
β-strand	728-732	5	33
α-helix	733-740	8
β-strand	746-749	4	33
β-strand	757-758	2	32
β-strand	761-763	3	28
α-helix	769-782	14
α-helix	784-792	9
α-helix	810-812	3
α-helix	813-840	28

Chain D: 33 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	36-42	7	35
α-helix	47-53	7
β-strand	67-73	7	35
α-helix	78-92	15
β-strand	97-100	4	35
α-helix	107-118	12
β-strand	123-127	5	35
α-helix	128-130	3
β-strand	143-145	3	35
α-helix	150-163	14
β-strand	168-174	7	36
α-helix	179-191	13
β-strand	198-205	8	36
α-helix	213-219	7
α-helix	220-222	3
β-strand	227-231	5	36
α-helix	234-247	14
β-strand	255-258	4	36
α-helix	260-263	4
α-helix	273-274	2
β-strand	278-282	5	36
α-helix	289-310	22
α-helix	326-329	4
α-helix	335-338	4
β-strand	343	1	37
β-strand	348	1	37
β-strand	351	1	38
β-strand	357	1	38
β-strand	362-366	5	36
β-strand	367	1	39
β-strand	373	1	39
β-strand	377-380	4	36
β-strand	383-386	4	36
α-helix	391-393	3
β-strand	405-410	6	40
β-strand	413	1	41
β-strand	417	1	41
β-strand	418-421	4	40
α-helix	422-423	2
β-strand	434-439	6	40
β-strand	452-458	7	40
α-helix	460-472	13
β-strand	475-480	6	40
β-strand	489-490	2	42
β-strand	493-494	2	42
α-helix	496-502	7
β-strand	508-509	2	40
β-strand	514	1	43
α-helix	519-521	3
β-strand	524-525	2	40
α-helix	526-528	3
β-strand	530-539	10	43
α-helix	549-551	3
α-helix	556-578	23
α-helix	603-611	9
α-helix	626-654	29
α-helix	669-672	4
β-strand	683-684	2	43
α-helix	690-698	9
α-helix	700-705	6
α-helix	706-709	4
α-helix	714-722	9
β-strand	728-732	5	43
α-helix	733-741	9
β-strand	748-750	3	43
β-strand	757-762	6	43
β-strand	765-766	2	40
α-helix	772-786	15
α-helix	788-796	9
α-helix	815-844	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A, C	protein	847	Rattus norvegicus	P35439 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2B	B, D	protein	883	Rattus norvegicus	Q00960 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7SAA_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
MSTMHLLTFALLFSCSFARAASDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQL
QATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLG
LTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYNWNHIILLVSDDHEGRAAQKRL
ETLLEERESKAEKVLQFDPGTKNVTALLMEARELEARVIILSASEDDAATVYRAAAMLDM
TGSGYVWLVGEREISGNALRYAPDGIIGLQLINGKNESAHISDAVGVVAQAVHELLEKEN
ITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFAQYSIMNLQNRK
LVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTMSDGTC
KEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMQFTYEVHLVA
DGKFGTQERVQNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTI
LVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDA
LTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRP
EERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQA
VRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQQVSLSILKSH
ENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRH
KDANGAQ

Sequence of entity 2 (B, D), FASTA

>7SAA_2 Glutamate receptor ionotropic, NMDA 2B (chains B, D)
MGTMRLFLLAVLFLFSFARATGWSHPQFEKGGGSGGGSGGSAWSHPQFEKGALVPRGRSQ
KSPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLM
SDRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPS
IEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSL
DDGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTV
PSEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRI
YQSNMLNRYLINVTFEGRNLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYY
VWPRMCPETEEQEDDHLSIVTLEEAPFVIVESVDPLSGTCMRNTVPCQKRIISENKTDEE
PGYIKKCCKGFCIDILKKISKSVKFTYDLYLVTNGKHGKKINGTWNGMIGEVVMKRAYMA
VGSLTINEERSEVVDFSVPFIETGISVMVSRSNGTVSPSAFLEPFSADVWVMMFVMLLIV
SAVAVFVFEYFSPVGYNRCLADGREPGGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSK
IMVSVWAFFAVIFLASYTANLAAFMIQEEYVDQVSGLSDKKFQRPNDFSPPFRFGTVPNG
STERNIRNNYAEMHAYMGKFNQRGVDDALLSLKTGKLDAFIYDAAVLNYMAGRDEGCKLV
TIGSGKVFASTGYGIAIQKDSGWKRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVM
SSQLDIDNMAGVFYMLGAAMALSLITFICEHLFYWQFRHSFMG

Ligands and cofactors

ID	Name	Formula	Copies
GLU	Glutamic acid	C5 H9 N O4	2
GLY	Glycine	C2 H5 N O2	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	8

Primary citation

Structural insights into binding of therapeutic channel blockers in NMDA receptors. Chou, T.H., Epstein, M., Michalski, K. et al. Nat Struct Mol Biol (2022) 29:507-518. DOI 10.1038/s41594-022-00772-0 · PubMed

Other PDB entries of the same protein (UniProt P35439 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1PB7 1.35 Å, Crystal structure of the NR1 ligand binding core in complex with glycine at 1.35 Å…
1Y20 1.4 Å, Crystal structure of the NR1 ligand-binding core in complex with ACPC
1PB8 1.45 Å, Crystal structure of the NR1 ligand binding core in complex with D-serine at 1.45 Å…
1Y1Z 1.5 Å, Crystal structure of the NR1 ligand binding core in complex with ACBC
5U8C 1.6 Å, Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and…
1PB9 1.6 Å, Crystal structure of the NR1 ligand binding core in complex with D-cycloserine at 1.60 Å…
6UZ6 1.66 Å, Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with…
5I57 1.7 Å, Glutamate- and glycine-bound GluN1/GluN2A agonist binding domains
9NYZ 1.71 Å, Crystal structure of DCKA/glutamate-bound GluN1/GluN2A agonist binding domains with…
1Y1M 1.8 Å, Crystal structure of the NR1 ligand binding core in complex with cycloleucine
4NF8 1.86 Å, Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and…
6UZR 1.87 Å, Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and…

Browse structure collections

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