5IOU: N-methyl-D-aspartate receptor subunit NR1-8a

Cryo-EM structure of GluN1/GluN2B NMDA receptor in the glutamate/glycine-bound conformation. Determined by electron microscopy at 7.0 Å resolution. Released 20 Apr 2016.

Method: Electron microscopy
Resolution: 7.0 Å
Organism: Xenopus laevis
Chains: 4
Atoms: 15,824
Mol. weight: 372.22 kDa
Ligands: GLU, GLY
Released: 20 Apr 2016

Explore 5IOU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IOU contains 112 α-helices and 160 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: 29 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	25-33	9	1
α-helix	36-52	17
β-strand	58-66	9	1
α-helix	71-77	7
α-helix	78-82	5
β-strand	87-92	6	1
α-helix	105-113	9
β-strand	118-120	3	1
α-helix	126-129	4
β-strand	137-139	3	1
α-helix	144-157	14
β-strand	162-163	2	2
β-strand	164-167	4	3
α-helix	171-183	13
β-strand	190-191	2	2
β-strand	195	1	3
α-helix	205-213	9
β-strand	218-222	5	3
α-helix	225-236	12
β-strand	246-248	3	3
α-helix	256-258	3
β-strand	267-271	5	3
α-helix	278-295	18
α-helix	319-326	8
β-strand	330	1	4
β-strand	338	1	4
β-strand	351-357	7	3
β-strand	360-363	4	3
β-strand	365-367	3	3
β-strand	372-374	3	3
α-helix	377-379	3
β-strand	397-402	6	5
β-strand	409-413	5	6
α-helix	414-415	2
α-helix	420-422	3
β-strand	424	1	7
β-strand	430	1	7
α-helix	431-432	2
β-strand	434-438	5	6
β-strand	449-455	7	6
α-helix	456-467	12
β-strand	471-476	6	5
β-strand	510-511	2	5
β-strand	515	1	8
α-helix	519-522	4
β-strand	526-527	2	9
β-strand	532-535	4	10
β-strand	536-537	2	11
α-helix	558-578	21
α-helix	592-604	13
α-helix	617-645	29
α-helix	660-663	4
β-strand	671-673	3	12
β-strand	674	1	13
α-helix	678-685	8
α-helix	693-697	5
β-strand	701	1	13
α-helix	704-712	9
β-strand	718-720	3	12
β-strand	721-722	2	11
α-helix	723-733	11
β-strand	745-748	4	10
β-strand	749	1	8
β-strand	751-752	2	9
α-helix	758-772	15
α-helix	774-782	9
α-helix	800-824	25

Chain B: 27 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	29-37	9	26
α-helix	43-46	4
β-strand	60-68	9	26
α-helix	73-86	14
β-strand	89-95	7	26
α-helix	101-114	14
β-strand	118-120	3	26
α-helix	124-126	3
β-strand	138-140	3	26
α-helix	145-157	13
β-strand	163-168	6	27
α-helix	175-185	11
β-strand	193-194	2	27
β-strand	198-199	2	27
α-helix	211-215	5
β-strand	222-226	5	27
α-helix	229-242	14
β-strand	250-253	4	27
β-strand	272-277	6	27
α-helix	284-305	22
α-helix	329-332	4
β-strand	339	1	28
β-strand	342	1	28
β-strand	346	1	29
β-strand	351	1	26
β-strand	352	1	29
β-strand	357-362	6	27
β-strand	368-372	5	27
β-strand	373-375	3	30
β-strand	378-380	3	30
β-strand	400-402	3	31
β-strand	411-413	3	32
α-helix	414-416	3
β-strand	427-429	3	32
β-strand	430	1	31
β-strand	432-433	2	33
β-strand	437	1	34
β-strand	440	1	34
β-strand	444-445	2	33
β-strand	448-451	4	32
α-helix	453-465	13
β-strand	470-472	3	31
β-strand	481-483	3	35
β-strand	486-488	3	35
α-helix	492-495	4
β-strand	501-502	2	31
β-strand	507	1	36
α-helix	512-515	4
β-strand	523-529	7	36
α-helix	538-541	4
α-helix	551-567	17
α-helix	579-596	18
α-helix	609-638	30
α-helix	643-645	3
α-helix	652-654	3
β-strand	666-667	2	37
β-strand	668	1	38
α-helix	673-681	9
α-helix	683-687	5
β-strand	693	1	38
α-helix	698-706	9
β-strand	711-712	2	37
β-strand	713-715	3	36
α-helix	716-724	9
β-strand	740-745	6	36
β-strand	748-749	2	31
α-helix	757-766	10
α-helix	771-778	8
α-helix	800-823	24

Chain C: 29 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	25-33	9	14
α-helix	36-52	17
β-strand	58-66	9	14
α-helix	71-77	7
α-helix	78-82	5
β-strand	87-91	5	14
α-helix	105-113	9
β-strand	118-120	3	14
α-helix	126-129	4
β-strand	137-139	3	14
α-helix	144-157	14
β-strand	163-167	5	15
α-helix	171-183	13
β-strand	191	1	15
β-strand	195	1	15
α-helix	205-213	9
β-strand	218-222	5	15
α-helix	225-236	12
β-strand	246-248	3	15
α-helix	256-258	3
β-strand	267-271	5	15
α-helix	278-295	18
α-helix	319-326	8
β-strand	329-330	2	16
β-strand	338-339	2	16
β-strand	351-357	7	15
β-strand	360-363	4	15
β-strand	365-367	3	15
β-strand	372-374	3	15
α-helix	377-379	3
β-strand	397	1	17
β-strand	400-402	3	18
β-strand	409-413	5	19
α-helix	414-415	2
α-helix	420-422	3
β-strand	424	1	20
β-strand	430	1	20
α-helix	431-432	2
β-strand	434-438	5	19
β-strand	449-455	7	19
α-helix	456-467	12
β-strand	471	1	17
β-strand	474-476	3	18
β-strand	510-511	2	18
β-strand	515-516	2	21
α-helix	519-522	4
β-strand	526-527	2	22
β-strand	533-537	5	23
α-helix	558-578	21
α-helix	592-604	13
α-helix	617-645	29
α-helix	660-663	4
β-strand	671-673	3	24
β-strand	674	1	25
α-helix	678-685	8
α-helix	693-697	5
β-strand	701	1	25
α-helix	704-712	9
β-strand	718-720	3	24
β-strand	721-722	2	23
α-helix	723-733	11
β-strand	743-747	5	23
β-strand	748-749	2	21
β-strand	751-752	2	22
α-helix	758-772	15
α-helix	774-782	9
α-helix	800-824	25

Chain D: 27 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	29-37	9	39
α-helix	43-46	4
β-strand	60-68	9	39
α-helix	73-86	14
β-strand	89-95	7	39
α-helix	101-114	14
β-strand	118-120	3	39
α-helix	124-126	3
β-strand	138-140	3	39
α-helix	145-158	14
β-strand	163-164	2	40
β-strand	165-168	4	41
α-helix	175-185	11
β-strand	193-194	2	40
β-strand	198-199	2	41
α-helix	211-215	5
β-strand	223-226	4	41
α-helix	230-242	13
β-strand	251-253	3	41
β-strand	273-277	5	41
α-helix	284-305	22
α-helix	329-332	4
β-strand	339	1	42
β-strand	342	1	42
β-strand	346	1	43
β-strand	351	1	39
β-strand	352	1	43
β-strand	357-362	6	41
β-strand	368-375	8	41
β-strand	378-380	3	41
β-strand	401-402	2	44
β-strand	411-413	3	45
α-helix	414-416	3
β-strand	427-429	3	45
β-strand	430	1	44
β-strand	432-433	2	46
β-strand	437	1	47
β-strand	440	1	47
β-strand	444-445	2	46
β-strand	448-451	4	45
α-helix	453-465	13
β-strand	472	1	44
β-strand	481-483	3	48
β-strand	486-488	3	48
α-helix	492-495	4
β-strand	501-502	2	44
β-strand	507	1	49
α-helix	512-515	4
β-strand	523-529	7	49
α-helix	537-539	3
α-helix	551-567	17
α-helix	579-596	18
α-helix	609-638	30
α-helix	643-645	3
α-helix	652-654	3
β-strand	666-667	2	50
β-strand	668	1	51
α-helix	673-681	9
α-helix	683-687	5
β-strand	693	1	51
α-helix	698-706	9
β-strand	711-712	2	50
β-strand	713-715	3	49
α-helix	716-724	9
β-strand	740-745	6	49
β-strand	748-749	2	44
α-helix	757-766	10
α-helix	771-778	8
α-helix	801-823	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-methyl-D-aspartate receptor subunit NR1-8a	A, C	protein	822	Xenopus laevis	A0A1L8F5J9 (AlphaFold model)
Ionotropic glutamate receptor subunit NR2B	B, D	protein	825	Xenopus laevis	A7XY94 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5IOU_1 N-methyl-D-aspartate receptor subunit NR1-8a (chains A, C)
DPKIVNIGAVLSTKKHEQIFREAVNQANFFHFTRKIQLNATSVTHRPNAIQMALSVCEDL
ISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVP
PYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEEKESKADKVLQFEPGTK
NLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYA
PDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMEQITDPPRGCVGNTNIWKTGPLFK
RVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFDGSYIIQNDRKIIWP
GGETERPQGYQMSTRLKIVTIHQEPFVYVRPTTSDGTCREEYTINGDPIKKVICNGPDET
IPGRPTVPQCCYGFCVDLLIKLAREMDFTYEVHLVADGKFGTQERVNNSNAAAWNGMMGE
LLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWL
LVGLSVHVVAVMLYLLDRFSPFGRFEDALTLSSAMWFSWRVLLNSGLGEGAPRSFSARIL
GMVWAGFAMIIVASYTANLAAFLVLRRPEERITGINDPRLRNPSDKFIYATVKQSSVDIY
FRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGEL
FFRSGFGIGMRKDSPWKQEVSLNILKSHENGFMEELDKTWVRYQECDSRSNAPATLTFEN
MAGVFMLVAGGIVAGIFLIFIEIAYKSRAEAKRMKGLEVLFQ

Sequence of entity 2 (B, D), FASTA

>5IOU_2 Ionotropic glutamate receptor subunit NR2B (chains B, D)
MRPTEACCYLKISLIILFYSRAYAQKHPNMDIAVILVGTTEEVAIKDVHEKDDFHHLPVT
PRVELVTMQESDPKSIITRICDLMSDKKVQGVVFGDDTDQEAIAQILDFISVQTLTPILG
IHGGSSMIMADKEEASMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFENK
VRSTIENSFVGWELEEVIHLDMSLDDIDSKIQNQLKKLQSPVILLYCTKEEATYIFEVAH
SVGLTGYGFTWIVPSLVAGDTDTVPDEFPTGLISVSYDEWDYDLPARVRDGIAIITTAAS
TMLSEHNSIPQSKSSCNNIQESRVYEAHMLKRYLINVTFEGRDLSFSEDGYQMHPKLVII
LLNQERKWERVGKYKDRSLKMWPVFDLYPNSEEHKDEHLSIVTLEEAPFVIVEDVDPLSG
TCMRNTVPCRKQIRPENRTEEGGNYIKRCCKGFCIDILKKIAKTVKFTYDLYLVTNGKHG
KKINGVWNGMIGEVVTKRAYMAVGSLTINEERSEVVDFSVPFIETGISVMVSRSNGTVSP
SAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNGPSFTIGKAIWLLWGLVFNNS
LPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQRRYVDQVSGLSDKKFQRPNDF
SPAFRFGTVPNGSTERNIRNNYLEMHSYMVKFNQRSVQDALLSLKSGKLDAFIYDAAVLN
YMAGRDEGCKLVTIGSGKVFATTGYGIAIQKDSGWKRQVDLAILQLFGDGEMEELEALWL
TGICHNEKNEVMSSQLDIDNMAGVFYMLAAAMALSLITFIMEHLF

Ligands and cofactors

ID	Name	Formula	Copies
GLU	Glutamic acid	C5 H9 N O4	2
GLY	Glycine	C2 H5 N O2	2

Primary citation

Mechanism of NMDA Receptor Inhibition and Activation. Zhu, S., Stein, R.A., Yoshioka, C. et al. Cell (2016) 165:704-714. DOI 10.1016/j.cell.2016.03.028 · PubMed

Other PDB entries of the same protein (UniProt A0A1L8F5J9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3QEK 2.0 Å, Crystal structure of amino terminal domain of the NMDA receptor subunit GluN1
6E7R 2.1 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
6E7U 2.27 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
6E7T 2.31 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
6E7X 2.58 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
3QEL 2.6 Å, Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and…
6E7V 2.6 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
6E7W 2.67 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
5TQ0 2.7 Å, Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and…
6E7S 2.72 Å, Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to…
9Q3Y 2.74 Å, GluN1b-GluN2B ATD in complex with radiprodil
5EWM 2.76 Å, Crystal structure of amino terminal domains of the nmda receptor subunit GLUN1 and…

Browse structure collections

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