5UP2: Triheteromeric NMDA receptor GluN1/GluN2A/GluN2B

Triheteromeric NMDA receptor GluN1/GluN2A/GluN2B in complex with glycine, glutamate, Ro 25-6981, MK-801 and a GluN2B-specific Fab, at pH 6.5. Determined by electron microscopy at 6.0 Å resolution. Released 22 Mar 2017.

Method: Electron microscopy
Resolution: 6.0 Å
Organisms: Xenopus laevis, Mus musculus
Chains: 6
Atoms: 24,161
Mol. weight: 414.92 kDa
Ligands: NAG
Released: 22 Mar 2017

Explore 5UP2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5UP2 contains 161 α-helices and 187 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: 36 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	26-32	7	1
α-helix	36-52	17
β-strand	59-65	7	1
α-helix	74-77	4
α-helix	78-83	6
β-strand	90-92	3	1
α-helix	106-114	9
β-strand	118-120	3	1
α-helix	127-129	3
β-strand	139	1	1
α-helix	145-147	3
α-helix	148-158	11
β-strand	164-168	5	2
α-helix	171-186	16
β-strand	194-197	4	2
α-helix	205-213	9
β-strand	218-222	5	2
α-helix	225-237	13
β-strand	246-249	4	2
α-helix	251-254	4
α-helix	256-259	4
β-strand	268-271	4	3
α-helix	277-297	21
α-helix	303-305	3
α-helix	318-326	9
β-strand	340	1	4
β-strand	346	1	4
β-strand	351-355	5	3
α-helix	357-359	3
β-strand	362-368	7	3
β-strand	371-374	4	3
α-helix	378-379	2
β-strand	397-401	5	5
β-strand	410-412	3	5
β-strand	415	1	6
β-strand	418	1	6
α-helix	423-425	3
β-strand	434-439	6	5
β-strand	448-454	7	5
α-helix	456-467	12
β-strand	471-474	4	5
β-strand	486	1	7
β-strand	494	1	7
α-helix	498-505	8
β-strand	510-511	2	5
α-helix	519-522	4
β-strand	526-527	2	5
α-helix	528-530	3
β-strand	533-539	7	8
α-helix	543-545	3
α-helix	550-558	9
α-helix	560-579	20
α-helix	601-613	13
α-helix	625-654	30
β-strand	679-680	2	9
β-strand	682	1	10
α-helix	687-693	7
α-helix	695-697	3
α-helix	698-705	8
β-strand	709	1	10
α-helix	712-721	10
β-strand	726-727	2	9
β-strand	728-730	3	8
α-helix	731-740	10
β-strand	746-755	10	8
β-strand	759-760	2	5
α-helix	767-779	13
α-helix	782-791	10
α-helix	797-798	2
α-helix	809-834	26

Chain B: 35 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	29-35	7	11
α-helix	42-56	15
β-strand	60-65	6	11
α-helix	71-84	14
β-strand	89-94	6	11
α-helix	100-112	13
β-strand	118	1	11
α-helix	121-124	4
α-helix	129-131	3
α-helix	143-157	15
β-strand	163-165	3	12
β-strand	166	1	13
α-helix	172-184	13
β-strand	197	1	13
α-helix	205-213	9
β-strand	218-221	4	12
α-helix	225-238	14
β-strand	246-249	4	12
α-helix	251-254	4
β-strand	269-270	2	12
α-helix	280-298	19
α-helix	317-319	3
α-helix	321-322	2
β-strand	332-335	4	14
β-strand	338-341	4	14
β-strand	342	1	15
β-strand	348	1	15
β-strand	353-358	6	12
β-strand	364-371	8	12
β-strand	374-377	4	12
α-helix	382-385	4
β-strand	394-398	5	16
β-strand	401	1	17
β-strand	405	1	17
β-strand	406-409	4	18
β-strand	411	1	19
β-strand	416	1	19
β-strand	422-426	5	18
α-helix	427-429	3
β-strand	439-445	7	18
α-helix	447-458	12
β-strand	463-466	4	16
β-strand	475-477	3	20
β-strand	480-482	3	20
α-helix	484-489	6
β-strand	495-497	3	16
α-helix	500-502	3
α-helix	504-509	6
β-strand	519	1	21
β-strand	521-524	4	22
α-helix	533-541	9
α-helix	542-546	5
α-helix	547-567	21
α-helix	585-587	3
α-helix	588-600	13
α-helix	613-643	31
α-helix	656-659	4
α-helix	661-663	3
β-strand	670-671	2	22
α-helix	677-683	7
α-helix	687-695	9
α-helix	701-710	10
β-strand	715-719	5	22
α-helix	720-729	10
β-strand	747	1	21
α-helix	760-772	13
α-helix	775-779	5
α-helix	780-784	5
α-helix	802-827	26

Chain C: 35 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	27-33	7	23
α-helix	36-52	17
β-strand	60-66	7	23
α-helix	71-76	6
α-helix	77-81	5
β-strand	90-92	3	23
α-helix	106-114	9
β-strand	118-120	3	23
α-helix	126-128	3
β-strand	137-139	3	23
α-helix	147-158	12
β-strand	164-168	5	24
α-helix	171-186	16
β-strand	194-197	4	24
α-helix	205-213	9
β-strand	218-222	5	24
α-helix	225-237	13
β-strand	246-249	4	24
α-helix	251-254	4
α-helix	257-260	4
α-helix	262-263	2
β-strand	267-271	5	24
α-helix	277-295	19
α-helix	301-305	5
α-helix	319-326	8
β-strand	340	1	25
β-strand	346	1	25
β-strand	351-355	5	24
β-strand	362-367	6	24
β-strand	372-374	3	24
α-helix	378-379	2
β-strand	399-402	4	26
β-strand	405	1	27
β-strand	409	1	27
β-strand	410-413	4	26
α-helix	420-422	3
β-strand	424	1	28
β-strand	430	1	28
β-strand	434-438	5	26
β-strand	449-454	6	26
α-helix	456-467	12
β-strand	473-476	4	26
α-helix	477	1
α-helix	478-480	3
β-strand	488	1	29
β-strand	492	1	29
α-helix	498-505	8
β-strand	510-511	2	26
β-strand	516	1	30
α-helix	519-522	4
β-strand	525-527	3	26
β-strand	532-541	10	30
α-helix	542-544	3
α-helix	549-581	33
α-helix	600-613	14
α-helix	625-652	28
α-helix	653-655	3
α-helix	668-671	4
β-strand	679-680	2	30
β-strand	682	1	31
α-helix	686-693	8
α-helix	699-704	6
β-strand	709	1	31
α-helix	712-720	9
β-strand	726-730	5	30
α-helix	731-740	10
β-strand	744-746	3	30
β-strand	751-756	6	30
β-strand	759-761	3	26
α-helix	767-780	14
α-helix	782-791	10
α-helix	805-835	31

Chain D: 39 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	29-37	9	32
α-helix	44-54	11
β-strand	60-68	9	32
α-helix	73-87	15
β-strand	91-96	6	32
α-helix	102-114	13
β-strand	118-120	3	32
α-helix	123-126	4
α-helix	131-133	3
β-strand	139-140	2	32
α-helix	145-158	14
β-strand	163-169	7	33
α-helix	174-187	14
β-strand	193-200	8	33
α-helix	207-216	10
β-strand	222-226	5	33
α-helix	229-242	14
β-strand	250-253	4	33
α-helix	255-258	4
α-helix	269	1
β-strand	273-277	5	33
α-helix	284-306	23
α-helix	319-321	3
α-helix	322-324	3
α-helix	327-335	9
β-strand	338-339	2	34
β-strand	342-343	2	34
β-strand	346	1	35
β-strand	351	1	32
β-strand	352	1	35
β-strand	357-362	6	33
β-strand	368-375	8	33
β-strand	378-379	2	33
β-strand	401-403	3	36
β-strand	406	1	37
β-strand	410	1	37
β-strand	411-414	4	38
α-helix	415-416	2
β-strand	427-429	3	38
β-strand	432-433	2	39
β-strand	444-445	2	39
α-helix	446	1
β-strand	448-451	4	38
α-helix	453-465	13
β-strand	471-473	3	36
β-strand	481-483	3	40
β-strand	486-488	3	40
α-helix	490-495	6
β-strand	501-502	2	36
α-helix	510-515	6
α-helix	519-521	3
β-strand	525	1	41
β-strand	527-531	5	42
α-helix	544-548	5
α-helix	551-565	15
α-helix	566-570	5
α-helix	571-573	3
α-helix	596-606	11
α-helix	620-648	29
α-helix	673-674	2
β-strand	676-677	2	42
α-helix	683-691	9
α-helix	693-699	7
α-helix	700-702	3
α-helix	707-715	9
β-strand	721-725	5	42
α-helix	726-734	9
β-strand	742-743	2	42
β-strand	753	1	41
α-helix	766-779	14
α-helix	781-785	5
α-helix	786-790	5
α-helix	797-799	3
α-helix	804-806	3
α-helix	810-835	26

Chain F: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	43
β-strand	10-13	4	44
β-strand	16	1	45
β-strand	19-25	7	43
β-strand	34-39	6	44
β-strand	45-50	6	44
β-strand	54-55	2	44
α-helix	56	1
β-strand	63-68	6	43
β-strand	71-76	6	43
β-strand	79	1	45
α-helix	81-83	3
β-strand	86-91	6	44
α-helix	97	1
β-strand	98-99	2	44
β-strand	103-107	5	44
α-helix	109-111	3
β-strand	112	1	46
β-strand	115-119	5	47
α-helix	123-127	5
β-strand	130-140	11	47
β-strand	141	1	46
β-strand	145-151	7	48
β-strand	154-156	3	48
β-strand	160-165	6	47
α-helix	166	1
β-strand	174-183	10	47
α-helix	184-188	5
β-strand	192-199	8	48
β-strand	206-211	6	48

Chain G: 8 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	217-221	5	49
β-strand	225-226	2	50
β-strand	232-239	8	49
β-strand	247-254	8	51
β-strand	258-266	9	51
α-helix	268-270	3
β-strand	271-274	4	51
α-helix	276-279	4
β-strand	282-287	6	49
β-strand	292-297	6	49
α-helix	302-304	3
β-strand	306-313	8	51
β-strand	322-323	2	51
β-strand	327-329	3	51
β-strand	330-331	2	50
α-helix	335-336	2
α-helix	338-339	2
β-strand	340-345	6	52
β-strand	346	1	47
α-helix	347	1
β-strand	351-361	11	52
β-strand	366-370	5	53
α-helix	371-373	3
β-strand	375	1	53
β-strand	379-387	9	52
β-strand	390-400	11	52
β-strand	404	1	54
β-strand	408	1	54
β-strand	410-415	6	53
α-helix	416-418	3
β-strand	420-425	6	53

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-methyl-D-aspartate receptor subunit NR1-8a	A, C	protein	836	Xenopus laevis	A0A1L8F5J9 (AlphaFold model)
N-methyl-D-aspartate receptor subunit NR2A	B	protein	831	Xenopus laevis	B7ZSK1 (AlphaFold model)
Ionotropic glutamate receptor subunit NR2B	D	protein	837	Xenopus laevis	A7XY94 (AlphaFold model)
GluN2B-specific Fab, termed 11D1	F, G	protein	216	Mus musculus

Sequence of entity 1 (A, C), FASTA

>5UP2_1 N-methyl-D-aspartate receptor subunit NR1-8a (chains A, C)
MGTMRLFLLAVLFLFSFARAGADPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQL
NATSVTHRPNAIQMALSVCEDLISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIG
LTTRMSIYSDKSIHLSFLRTVPPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKL
ETLLEEKESKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDM
TGAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMEQ
ITDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRK
LVQVGIFDGSYIIQNDRKIIWPGGETERPQGYQMSTRLKIVTIHQEPFVYVRPTTSDGTC
REEYTINGDPIKKVICNGPDETIPGRPTVPQCCYGFCVDLLIKLAREMDFTYEVHLVADG
KFGTQERVNNSNAAAWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILV
KKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSAAAEEDALT
LSSAMWFSWRVLLNSGLGEGAPRSFSARILGMVWALFAMIIVASYTANLAAFLVLRRPEE
RITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQAVR
DNKLHAFIWDSAVLEFEASQDCDLVTTGELFFRSGFGIGMRKDSPWKQEVSLNILKSHEN
GFMEELDKTWVRYQECDSRSNAPATLTFENMAGVFYLVAGGIVAGIFLIFIEIAYK

Sequence of entity 2 (B), FASTA

>5UP2_2 N-methyl-D-aspartate receptor subunit NR2A (chains B)
MGMFVLLLYTFLYAGDLGHGAEKSFPVLNIAVILGRTRYITERDIRSLWTRDMSLDFDVN
VVTLLVQQTDPKSIITHVCDLMSGTKIHGVVFGDDTDQEAIAQILDFVSSQTFIPILGIH
GGSSMIMADKDEMSTFFQFGASIKQQATVMLNIMEEYDWHVFSVITSNFPGYRDFISFIK
TTVDNSFVGWEVQNYITLDTSYTDAQTLTQLKKIHSSVILLYCSKDEATYIFEEARSLGL
MGYGFVWIVPSLVTGNTDIIPYEFPSGLVSVSYDDWDYGIEARVRDGLGIITTAASAMLE
KHSVIPEAKTSCYGQNERNDPPLHTLHNFMINVTWDGKDLSFTEDGYQANPKLVVLLLNM
EREWEKVGKWEAKSLNMKYPVWPRIDSDHDDNHLSIVTLEEAPFVIVENIDYLTGTCVRN
TVPCRKYFRLANSTTEGTSVKKCCKGFCIDILKKLSKTVKFTYDLYLVTNGKHGKKIKNV
WNGMIGEVVYKRAVMAVGSLTINEERSVAVDFSVPFVETGISVMVSRSAGTVSPSAFLEP
FSASVWVMMFVMLLLVSAMAVFIFEYFSPVGYNRNLAQGKDPHGPSFTIGKAVWLLWGLV
FNNSLPVQNPKGTTSKIIVSIWAFFAVIFLASYTANLAAFMIQRRFVDQVTGLSDNKFQR
PHDYSPPFRFGTVPQGSTERNIRNNYPDMHQYMVKFHQKGVQDALVSLKTGKLDAFIYDA
AVLNYMAGRDEGCKLVTIGSGYIFATTGYGIALQKGSRWKRPIDLALLQFVGDGEMEELE
KLWLTGICHTEKNEVMSSQLDIDNMAGVFYMLAAAMALSLITFVWEHLFYK

Sequence of entity 3 (D), FASTA

>5UP2_3 Ionotropic glutamate receptor subunit NR2B (chains D)
MRPTEACCYLKISLIILFYSRAYAQKHPNMDIAVILVGTTEEVAIKDVHEKDDFHHLPVT
PRVELVTMQESDPKSIITRICDLMSDKKVQGVVFGDDTDQEAIAQILDFISVQTLTPILG
IHGGSSMIMADKEEASMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFENK
VRSTIENSFVGWELEEVIHLDMSLDDIDSKIQNQLKKLQSPVILLYCTKEEATYIFEVAH
SVGLTGYGFTWIVPSLVAGDTDTVPDEFPTGLISVSYDEWDYDLPARVRDGIAIITTAAS
TMLSEHNSIPQSKSSCNNIQESRVYEAHMLKRYLINVTFEGRDLSFSEDGYQMHPKLVII
LLNQERKWERVGKYKDRSLKMWPVFDLYPNSEEHKDEHLSIVTLEEAPFVIVEDVDPLSG
TCMRNTVPCRKQIRPENRTEEGGNYIKRCCKGFCIDILKKIAKTVKFTYDLYLVTNGKHG
KKINGVWNGMIGEVVTKRAYMAVGSLTINEERSEVVDFSVPFIETGISVMVSRSNGTVSP
SAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNRALADGREPGGPSFTIGKAIW
LLWGLVFNNSLPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQRRYVDQVSGLS
DKKFQRPNDFSPAFRFGTVPNGSTERNIRNNYLEMHSYMVKFNQRSVQDALLSLKSGKLD
AFIYDAAVLNYMAGRDEGCKLVTIGSGKVFATTGYGIAIQKDSGWKRQVDLAILQLFGDG
EMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLAAAMALSLITFIMEHLFYK

Sequence of entity 4 (F, G), FASTA

>5UP2_4 GluN2B-specific Fab, termed 11D1 (chains F, G)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Cryo-EM structures of the triheteromeric NMDA receptor and its allosteric modulation. Lu, W., Du, J., Goehring, A. et al. Science (2017) 355. DOI 10.1126/science.aal3729 · 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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