5UN1: GluN1/GluN2B delta-ATD NMDA receptor

Crystal structure of GluN1/GluN2B delta-ATD NMDA receptor. Determined by X-ray diffraction at 3.6 Å resolution. Released 7 Feb 2018.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: Xenopus laevis
Chains: 8
Atoms: 20,143
Mol. weight: 408.4 kDa
Ligands: GLY, NAG, GLU, BMK
Released: 7 Feb 2018

Explore 5UN1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5UN1 contains 147 α-helices and 157 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: 20 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	397-402	6	8
β-strand	405	1	9
β-strand	409	1	9
β-strand	410-412	3	10
α-helix	413-415	3
α-helix	420-422	3
β-strand	424	1	11
β-strand	430	1	11
α-helix	431-432	2
β-strand	434-439	6	10
α-helix	440-442	3
β-strand	448-454	7	10
α-helix	456-467	12
β-strand	471-476	6	8
β-strand	483-486	4	12
β-strand	495-498	4	12
α-helix	499-504	6
β-strand	511-516	6	8
α-helix	517	1
α-helix	519-522	4
β-strand	526-527	2	8
β-strand	532-533	2	8
β-strand	536-540	5	13
β-strand	546	1	14
α-helix	558-578	21
α-helix	593-605	13
α-helix	617-643	27
α-helix	650-652	3
α-helix	660-663	4
β-strand	671-672	2	13
β-strand	674	1	15
α-helix	678-685	8
α-helix	690-697	8
β-strand	701	1	15
α-helix	704-712	9
β-strand	718-722	5	13
α-helix	723-732	10
β-strand	737-738	2	13
β-strand	743	1	13
β-strand	747-752	6	8
α-helix	758-771	14
α-helix	774-782	9
β-strand	798	1	14
β-strand	799	1	16
α-helix	802-825	24

Chain B: 17 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	398-403	6	17
β-strand	411-413	3	17
α-helix	414-416	3
β-strand	427-431	5	17
β-strand	446-451	6	17
α-helix	453-464	12
β-strand	468-473	6	17
β-strand	481-483	3	18
β-strand	486-488	3	18
α-helix	490-495	6
β-strand	501-502	2	17
β-strand	507	1	19
α-helix	510-515	6
β-strand	517-525	9	17
β-strand	527-530	4	20
α-helix	545-547	3
α-helix	550-570	21
α-helix	585-596	12
α-helix	604-605	2
α-helix	609-636	28
β-strand	666-667	2	20
α-helix	676-681	6
α-helix	683-689	7
α-helix	697-705	9
β-strand	711-715	5	20
α-helix	716-724	9
α-helix	727-729	3
β-strand	733	1	20
β-strand	743-749	7	17
α-helix	756-769	14
α-helix	771-779	9
α-helix	798-826	29

Chain C: 18 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	397-402	6	41
β-strand	409-412	4	42
α-helix	413-415	3
α-helix	420-422	3
β-strand	424	1	43
β-strand	430	1	43
α-helix	431-432	2
β-strand	434-439	6	42
β-strand	448-455	8	42
α-helix	456-467	12
β-strand	471-476	6	41
β-strand	483-486	4	44
β-strand	495-498	4	44
α-helix	499-504	6
β-strand	510-516	7	41
α-helix	517	1
α-helix	519-522	4
β-strand	525-527	3	41
β-strand	532-541	10	41
α-helix	558-581	24
α-helix	593-604	12
α-helix	617-643	27
α-helix	660-663	4
β-strand	671-672	2	41
β-strand	674	1	45
α-helix	678-685	8
α-helix	689-697	9
β-strand	701	1	45
α-helix	704-712	9
β-strand	718-722	5	41
α-helix	723-730	8
β-strand	736-738	3	41
β-strand	743-753	11	41
α-helix	758-772	15
α-helix	774-782	9
α-helix	800-824	25

Chain D: 16 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	398-403	6	46
β-strand	411-414	4	47
α-helix	415-416	2
β-strand	427-432	6	47
β-strand	445-451	7	47
α-helix	453-465	13
β-strand	468-473	6	46
β-strand	481-483	3	48
β-strand	486-488	3	48
α-helix	490-495	6
β-strand	501-502	2	49
β-strand	507	1	50
α-helix	512-514	3
β-strand	516-518	3	49
β-strand	523-524	2	50
β-strand	527-532	6	51
β-strand	547	1	16
α-helix	549-570	22
α-helix	586-596	11
α-helix	603-606	4
α-helix	609-636	28
β-strand	666-667	2	51
α-helix	673-681	9
α-helix	683-691	9
α-helix	697-705	9
β-strand	711-715	5	51
α-helix	718-724	7
β-strand	731-733	3	51
α-helix	734-737	4
β-strand	744-745	2	50
β-strand	748-750	3	49
α-helix	757-769	13
α-helix	771-779	9
α-helix	801-827	27

Chain E: 19 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	398-402	5	27
β-strand	405	1	28
β-strand	409	1	28
β-strand	410-412	3	29
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	29
β-strand	448-454	7	29
α-helix	456-467	12
β-strand	472-476	5	27
β-strand	483-486	4	31
β-strand	495-498	4	31
α-helix	499-504	6
β-strand	510-511	2	27
α-helix	515	1
β-strand	516	1	32
α-helix	517	1
α-helix	519-522	4
β-strand	526-527	2	27
β-strand	532-540	9	32
β-strand	556	1	33
α-helix	558-578	21
α-helix	592-605	14
α-helix	617-643	27
α-helix	648-651	4
α-helix	660-663	4
β-strand	671-672	2	32
β-strand	674	1	34
α-helix	678-685	8
α-helix	690-698	9
β-strand	701	1	34
α-helix	704-712	9
β-strand	718-722	5	32
α-helix	723-732	10
β-strand	737	1	32
β-strand	743-748	6	32
β-strand	751-752	2	27
α-helix	758-771	14
α-helix	774-782	9
α-helix	800-819	20

Chain F: 20 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	398-403	6	35
β-strand	411-414	4	35
α-helix	415-416	2
β-strand	427-432	6	35
β-strand	445-451	7	35
α-helix	453-464	12
β-strand	468-473	6	35
β-strand	482-483	2	36
β-strand	486-487	2	36
α-helix	490-495	6
β-strand	502	1	37
β-strand	507	1	38
α-helix	510-515	6
β-strand	517-518	2	37
β-strand	524	1	39
β-strand	527-532	6	40
α-helix	550	1
α-helix	551-556	6
α-helix	557-570	14
α-helix	589-596	8
α-helix	604-606	3
α-helix	611-636	26
α-helix	673-681	9
α-helix	683-691	9
α-helix	697-705	9
β-strand	712-715	4	40
α-helix	716-725	10
β-strand	731-733	3	40
α-helix	734-737	4
β-strand	744	1	39
β-strand	745	1	38
β-strand	748-749	2	37
α-helix	756-768	13
α-helix	771-775	5
α-helix	776-780	5
α-helix	783-786	4
β-strand	796	1	33
α-helix	798-826	29

Chain G: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	398-402	5	1
β-strand	410-412	3	2
α-helix	413-415	3
α-helix	420-421	2
β-strand	424-425	2	3
β-strand	429-430	2	3
α-helix	431-432	2
β-strand	434-439	6	2
β-strand	448-454	7	2
α-helix	456-467	12
β-strand	472-476	5	1
β-strand	484-486	3	4
β-strand	495-497	3	4
α-helix	499-504	6
β-strand	510-511	2	1
α-helix	519-522	4
β-strand	525-527	3	1
α-helix	528	1
α-helix	530	1
β-strand	532-533	2	5
β-strand	536-541	6	6
α-helix	558-578	21
α-helix	579-581	3
α-helix	593-604	12
α-helix	617-643	27
α-helix	650-652	3
α-helix	660-663	4
β-strand	671-672	2	6
β-strand	674	1	7
α-helix	678-685	8
α-helix	690-699	10
β-strand	701	1	7
α-helix	704-712	9
β-strand	718-722	5	6
α-helix	723-730	8
β-strand	736-743	8	6
β-strand	747-748	2	5
β-strand	751-753	3	1
α-helix	758-771	14
α-helix	774-782	9
α-helix	800-825	26

Chain H: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	401-403	3	21
β-strand	411-413	3	21
α-helix	414-415	2
β-strand	416	1	22
β-strand	421	1	22
β-strand	427-432	6	21
β-strand	445-451	7	21
α-helix	453-464	12
β-strand	471-473	3	21
β-strand	480-483	4	23
β-strand	486-489	4	23
α-helix	490-495	6
β-strand	501-502	2	21
β-strand	507	1	24
α-helix	510-515	6
β-strand	517-518	2	21
β-strand	524	1	25
β-strand	527-531	5	26
α-helix	551-569	19
α-helix	584-596	13
α-helix	614-636	23
α-helix	652-655	4
α-helix	673-681	9
α-helix	683-691	9
α-helix	697-705	9
β-strand	711-715	5	26
α-helix	716-724	9
α-helix	727-729	3
β-strand	732-733	2	26
β-strand	740	1	26
β-strand	744	1	25
β-strand	745	1	24
β-strand	748-749	2	21
α-helix	756-769	14
α-helix	771-779	9
α-helix	800-822	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-methyl-D-aspartate receptor subunit NR1-3a	A, C, E, G	protein	451	Xenopus laevis	A0A1L8F5J9 (AlphaFold model)
Ionotropic glutamate receptor subunit NR2B	B, D, F, H	protein	448	Xenopus laevis	A7XY94 (AlphaFold model)

Sequence of entity 1 (A, C, E, G), FASTA

>5UN1_1 N-methyl-D-aspartate receptor subunit NR1-3a (chains A, C, E, G)
MSTRLKIVTIHQEPFVYVRPTTSDGTCREEYTINGDPIKKVICNGPDETIPGRPTVPQCC
YGFCVDLLIKLAREMDFTYEVHLVADGKFGTQERVNNSNAAAWNGMMGELLSGQADMIVA
PLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAV
MLYLLDRFSPFGRFEDALTLSSAMWFSWRVLLNSGLGEGAPRSFSARILGMVWAGFAMII
VASYTANLAAFLVLRRPEERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMY
RHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMR
KDSPWKQEVSLNILKSHENGFMEELDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGG
IVAGIFLIFIEIAYKSRAEAKRMKGLEVLFQ

Sequence of entity 2 (B, D, F, H), FASTA

>5UN1_2 Ionotropic glutamate receptor subunit NR2B (chains B, D, F, H)
DEHLSIVTLEEAPFVIVEDVDPLSGTCMRNTVPCRKQIRPENRTEEGGNYIKRCCKGFCI
DILKKIAKTVKFTYDLYLVTNGKHGKKINGVWNGMIGEVVTKRAYMAVGSLTINEERSEV
VDFSVPFIETGISVMVSRSNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSP
VGYNGPSFTIGKAIWLLWGLVFNNSLPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAA
FMIQRRYVDQVSGLSDKKFQRPNDFSPAFRFGTVPNGSTERNIRNNYLEMHSYMVKFNQR
SVQDALLSLKSGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKVFATTGYGIAIQKDSGW
KRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLAAAMALS
LITFIMEHLFYKSRAEAKRMKGLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
GLY	Glycine	C2 H5 N O2	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6
GLU	Glutamic acid	C5 H9 N O4	5
BMK	(5S,10R)-5-methyl-10,11-dihydro-5H-5,10-epiminodibenzo[a,d][7]annulene	C16 H15 N	2
MG	Magnesium ion	Mg	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	1

Water and common crystallization additives (TRS) are not listed.

Primary citation

Mechanism of NMDA receptor channel block by MK-801 and memantine. Song, X., Jensen, M.O., Jogini, V. et al. Nature (2018) 556:515-519. DOI 10.1038/s41586-018-0039-9 · 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…

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