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

Cryo-EM structure of GluN1/GluN2B NMDA receptor in the glutamate/glycine/Ro25-6981-bound conformation. Determined by electron microscopy at 7.5 Å resolution. Released 20 Apr 2016.

Method: Electron microscopy
Resolution: 7.5 Å
Organism: Xenopus laevis
Chains: 4
Atoms: 15,879
Mol. weight: 372.9 kDa
Ligands: GLU, QEM, GLY
Released: 20 Apr 2016

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

Secondary structure: helices and β-sheets

5IOV contains 111 α-helices and 149 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, 35 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	163-167	5	2
α-helix	171-183	13
β-strand	191	1	2
β-strand	195	1	2
α-helix	205-213	9
β-strand	218-222	5	2
α-helix	225-236	12
β-strand	246-248	3	2
β-strand	267-271	5	2
α-helix	278-295	18
α-helix	319-326	8
β-strand	330	1	3
β-strand	338	1	3
β-strand	351-357	7	2
β-strand	360-363	4	2
β-strand	365-367	3	2
β-strand	372-374	3	2
α-helix	377-379	3
β-strand	398-402	5	4
β-strand	409-413	5	5
α-helix	414-415	2
α-helix	420-422	3
β-strand	424	1	6
β-strand	430	1	6
α-helix	431-432	2
β-strand	434-438	5	5
β-strand	449-455	7	5
α-helix	456-466	11
β-strand	472-476	5	4
β-strand	510-511	2	4
β-strand	516	1	7
α-helix	519-522	4
β-strand	526-527	2	8
β-strand	532-537	6	7
α-helix	558-578	21
α-helix	592-604	13
α-helix	617-646	30
α-helix	660-663	4
β-strand	671-673	3	9
β-strand	674	1	10
α-helix	678-685	8
α-helix	693-697	5
β-strand	701	1	10
α-helix	704-712	9
β-strand	718-720	3	9
β-strand	721-722	2	7
α-helix	723-733	11
β-strand	743-748	6	7
β-strand	751-752	2	8
α-helix	759-772	14
α-helix	774-782	9
α-helix	795-797	3
α-helix	800-824	25

Chain B: 28 helices, 39 β-strands

Element	Residues	Length	Sheet
β-strand	29-37	9	22
α-helix	43-46	4
α-helix	52-54	3
β-strand	60-68	9	22
α-helix	73-86	14
β-strand	89	1	22
β-strand	93-95	3	22
α-helix	101-114	14
β-strand	118-120	3	22
α-helix	124-126	3
β-strand	138-140	3	22
α-helix	145-158	14
β-strand	163-168	6	23
α-helix	175-185	11
β-strand	193-199	7	23
α-helix	211-215	5
β-strand	222-226	5	23
α-helix	229-241	13
β-strand	250-252	3	23
α-helix	269	1
β-strand	273-277	5	23
α-helix	284-305	22
α-helix	329-332	4
β-strand	339	1	24
β-strand	342	1	24
β-strand	351	1	22
β-strand	356-362	7	23
β-strand	368-375	8	23
β-strand	379-380	2	23
β-strand	401-402	2	25
β-strand	411-413	3	26
α-helix	414-416	3
β-strand	427-429	3	26
β-strand	430	1	25
β-strand	432-433	2	27
β-strand	437	1	28
β-strand	440	1	28
β-strand	444-445	2	27
β-strand	448-451	4	26
α-helix	453-465	13
β-strand	472	1	25
β-strand	481-483	3	29
β-strand	486-488	3	29
α-helix	492-495	4
β-strand	501-502	2	25
β-strand	507	1	30
α-helix	512-515	4
β-strand	523-529	7	30
α-helix	537-541	5
α-helix	551-567	17
α-helix	579-596	18
α-helix	609-638	30
α-helix	652-654	3
β-strand	666-667	2	31
β-strand	668	1	32
α-helix	673-681	9
α-helix	683-687	5
β-strand	693	1	32
α-helix	698-706	9
β-strand	711-712	2	31
β-strand	713-715	3	30
α-helix	716-724	9
β-strand	740-745	6	30
β-strand	748-749	2	25
α-helix	757-766	10
α-helix	771-776	6
α-helix	800-823	24

Chain C: 27 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	25-33	9	11
α-helix	36-52	17
β-strand	58-66	9	11
α-helix	71-79	9
β-strand	87-91	5	11
α-helix	105-113	9
β-strand	118-120	3	11
α-helix	126-129	4
β-strand	137-139	3	11
α-helix	144-157	14
β-strand	163-167	5	12
α-helix	171-183	13
β-strand	191-195	5	12
α-helix	205-213	9
β-strand	218-222	5	12
α-helix	225-236	12
β-strand	246-248	3	12
α-helix	256-258	3
β-strand	267-271	5	12
α-helix	278-295	18
α-helix	317-326	10
β-strand	329-330	2	13
β-strand	338-339	2	13
β-strand	351-357	7	12
β-strand	360-363	4	12
β-strand	365-367	3	12
β-strand	372-374	3	12
α-helix	377-379	3
β-strand	397-402	6	14
β-strand	409-413	5	15
α-helix	414-415	2
α-helix	420-422	3
β-strand	424	1	16
β-strand	430	1	16
β-strand	434-438	5	15
β-strand	449-455	7	15
α-helix	456-466	11
β-strand	471-476	6	14
β-strand	510-511	2	14
β-strand	515-516	2	17
α-helix	519-522	4
β-strand	526-527	2	18
β-strand	533-535	3	19
β-strand	536-537	2	20
α-helix	558-577	20
α-helix	592-604	13
α-helix	617-646	30
α-helix	660-663	4
β-strand	674	1	21
α-helix	678-685	8
α-helix	693-697	5
β-strand	701	1	21
α-helix	704-712	9
β-strand	721-722	2	20
α-helix	723-733	11
β-strand	745-747	3	19
β-strand	748-749	2	17
β-strand	751-752	2	18
α-helix	758-772	15
α-helix	774-782	9
α-helix	800-824	25

Chain D: 27 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	29-37	9	33
α-helix	43-46	4
α-helix	52-54	3
β-strand	60-68	9	33
α-helix	73-86	14
β-strand	89-95	7	33
α-helix	102-114	13
β-strand	118-120	3	33
α-helix	124-126	3
β-strand	138-140	3	33
α-helix	145-158	14
β-strand	163-164	2	34
β-strand	165-168	4	35
α-helix	175-185	11
β-strand	193-194	2	34
β-strand	198-199	2	35
α-helix	211-215	5
β-strand	222-226	5	35
α-helix	229-242	14
β-strand	250-253	4	35
β-strand	272-276	5	35
α-helix	284-305	22
α-helix	329-332	4
β-strand	339	1	36
β-strand	342	1	36
β-strand	346	1	37
β-strand	352	1	37
β-strand	357-362	6	35
β-strand	368-374	7	35
β-strand	379-380	2	35
β-strand	401-402	2	38
β-strand	411-413	3	39
α-helix	414-416	3
β-strand	427-429	3	39
β-strand	430	1	38
β-strand	432-433	2	40
β-strand	437	1	41
β-strand	440	1	41
β-strand	444-445	2	40
β-strand	448-451	4	39
α-helix	453-465	13
β-strand	472	1	38
β-strand	481-483	3	42
β-strand	486-488	3	42
α-helix	492-495	4
β-strand	501-502	2	38
β-strand	507	1	43
α-helix	512-515	4
β-strand	523-529	7	43
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	44
β-strand	668	1	45
α-helix	673-681	9
α-helix	683-687	5
β-strand	693	1	45
α-helix	697-706	10
β-strand	711-712	2	44
β-strand	713-715	3	43
α-helix	716-724	9
β-strand	740-745	6	43
β-strand	748-749	2	38
α-helix	758-766	9
α-helix	771-778	8
α-helix	800-823	24

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

>5IOV_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

>5IOV_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
QEM	4-[(1R,2S)-3-(4-benzylpiperidin-1-yl)-1-hydroxy-2-methylpropyl]phenol	C22 H29 N O2	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

About this viewer

MolViewer shows 5IOV 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.