4TLL: GluN1/GluN2B NMDA receptor, structure 1

Crystal structure of GluN1/GluN2B NMDA receptor, structure 1. Determined by X-ray diffraction at 3.59 Å resolution. Released 2 Jul 2014.

Method: X-ray diffraction
Resolution: 3.59 Å
Organism: Xenopus laevis
Chains: 4
Atoms: 18,759
Mol. weight: 373.45 kDa
Ligands: NAG, 1AC, QEM, JEG
Released: 2 Jul 2014

Explore 4TLL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4TLL contains 139 α-helices and 152 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: 37 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	24	1
β-strand	25-33	9	1
α-helix	36-51	16
β-strand	58-66	9	1
α-helix	67-68	2
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-85	3
β-strand	87-92	6	1
α-helix	104-113	10
β-strand	118-120	3	1
α-helix	126-128	3
β-strand	137-139	3	1
α-helix	147-157	11
β-strand	163-168	6	2
α-helix	171-184	14
β-strand	191-197	7	2
α-helix	205-212	8
β-strand	218-222	5	2
α-helix	225-237	13
β-strand	246-249	4	2
α-helix	257-261	5
α-helix	262-263	2
β-strand	267-271	5	2
α-helix	277-295	19
α-helix	302-305	4
α-helix	314-315	2
α-helix	318-326	9
β-strand	330	1	3
β-strand	338	1	3
β-strand	339-340	2	4
β-strand	346-347	2	4
β-strand	351-356	6	2
β-strand	361-368	8	2
β-strand	371-374	4	2
α-helix	378-379	2
β-strand	398-402	5	5
β-strand	405	1	6
β-strand	409	1	6
β-strand	410-413	4	5
α-helix	414-415	2
α-helix	419-422	4
β-strand	424	1	7
β-strand	430	1	7
α-helix	431-432	2
β-strand	434-439	6	5
β-strand	448-454	7	5
α-helix	456-467	12
β-strand	472-476	5	5
β-strand	483-486	4	8
β-strand	495-498	4	8
α-helix	499-504	6
β-strand	510-511	2	5
β-strand	516	1	9
α-helix	519-524	6
β-strand	526-527	2	5
α-helix	528-530	3
β-strand	532-541	10	9
α-helix	559-580	22
α-helix	594-604	11
α-helix	617-645	29
α-helix	660-663	4
β-strand	671-672	2	9
β-strand	674	1	10
α-helix	678-685	8
α-helix	690-699	10
β-strand	701	1	10
α-helix	704-712	9
β-strand	718-722	5	9
α-helix	723-732	10
β-strand	736-738	3	9
β-strand	743-748	6	9
β-strand	751-752	2	5
α-helix	758-772	15
α-helix	774-782	9
α-helix	812-830	19

Chain B: 34 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	29-37	9	11
β-strand	60-68	9	11
α-helix	73-84	12
β-strand	89-95	7	11
α-helix	102-114	13
β-strand	118-120	3	11
α-helix	123-126	4
α-helix	131-133	3
β-strand	138-140	3	11
β-strand	143	1	12
α-helix	144	1
α-helix	145-158	14
β-strand	163-169	7	13
α-helix	174-186	13
β-strand	193-200	8	13
α-helix	210-216	7
β-strand	222-226	5	13
α-helix	229-242	14
β-strand	250-253	4	13
α-helix	255-258	4
α-helix	269	1
β-strand	273-277	5	13
α-helix	284-305	22
α-helix	319-321	3
α-helix	324-335	12
β-strand	338-339	2	14
β-strand	342-343	2	14
β-strand	346	1	12
β-strand	352	1	12
β-strand	357-362	6	13
β-strand	368-374	7	13
β-strand	379-380	2	13
β-strand	400-403	4	15
β-strand	411-414	4	15
α-helix	415-416	2
β-strand	427-431	5	15
β-strand	447-451	5	15
α-helix	453-464	12
β-strand	470-473	4	15
β-strand	482	1	16
β-strand	487	1	16
α-helix	489-495	7
β-strand	502-503	2	17
α-helix	510-515	6
β-strand	517-518	2	17
α-helix	519-521	3
β-strand	524	1	18
β-strand	527-532	6	19
α-helix	545-547	3
α-helix	550-568	19
α-helix	588-596	9
α-helix	611-639	29
α-helix	650-654	5
α-helix	657-659	3
α-helix	663-665	3
α-helix	673-681	9
α-helix	683-689	7
α-helix	697-705	9
β-strand	711-715	5	19
α-helix	716-724	9
α-helix	727-729	3
β-strand	731-733	3	19
β-strand	740	1	19
β-strand	744	1	18
β-strand	747-749	3	17
α-helix	755-769	15
α-helix	771-780	10
α-helix	806-825	20

Chain C: 37 helices, 38 β-strands

Element	Residues	Length	Sheet
β-strand	25-29	5	20
β-strand	30-33	4	21
α-helix	36-51	16
β-strand	58-62	5	20
β-strand	65-66	2	21
α-helix	67-68	2
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-85	3
β-strand	90-92	3	21
α-helix	94-95	2
α-helix	105-113	9
β-strand	118-120	3	21
α-helix	126-128	3
β-strand	137-139	3	21
α-helix	145-147	3
α-helix	148-158	11
β-strand	164-168	5	22
α-helix	171-184	14
β-strand	193-197	5	22
α-helix	205-213	9
β-strand	218-222	5	22
α-helix	225-237	13
β-strand	246-249	4	22
α-helix	257-260	4
α-helix	262-263	2
β-strand	267-271	5	22
α-helix	278-295	18
α-helix	301-305	5
α-helix	314-315	2
α-helix	318-326	9
β-strand	339-340	2	23
β-strand	346-347	2	23
β-strand	351-356	6	22
β-strand	361-367	7	22
β-strand	373-374	2	22
α-helix	378-379	2
β-strand	398-402	5	24
β-strand	405	1	24
β-strand	409-413	5	24
α-helix	414-415	2
α-helix	419-422	4
β-strand	424	1	25
β-strand	430	1	25
α-helix	431-432	2
β-strand	434-438	5	24
β-strand	449-455	7	24
α-helix	456-467	12
β-strand	472-476	5	24
β-strand	483-485	3	26
β-strand	496-498	3	26
α-helix	499-504	6
β-strand	510-511	2	24
β-strand	516	1	27
α-helix	519-522	4
β-strand	527	1	24
α-helix	528	1
α-helix	530	1
β-strand	532-541	10	27
α-helix	559-578	20
α-helix	619-646	28
α-helix	660-663	4
β-strand	671-673	3	27
β-strand	674	1	28
α-helix	678-685	8
α-helix	690-699	10
β-strand	701	1	28
α-helix	704-712	9
β-strand	718-722	5	27
α-helix	723-732	10
β-strand	736-738	3	27
β-strand	743-748	6	27
β-strand	751	1	24
α-helix	758-772	15
α-helix	774-783	10

Chain D: 31 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	29-37	9	29
β-strand	60-68	9	29
α-helix	73-84	12
β-strand	89-95	7	29
α-helix	102-114	13
β-strand	118-120	3	29
α-helix	123-126	4
β-strand	138-140	3	29
β-strand	143	1	30
α-helix	144	1
α-helix	145-158	14
β-strand	163-169	7	31
α-helix	174-187	14
β-strand	190	1	32
β-strand	193-200	8	31
α-helix	210-215	6
β-strand	222-226	5	31
α-helix	229-242	14
β-strand	250-252	3	31
α-helix	269	1
β-strand	273-277	5	31
α-helix	284-305	22
α-helix	324-335	12
β-strand	338-339	2	33
β-strand	342-343	2	33
β-strand	346	1	30
β-strand	352	1	30
β-strand	357-362	6	31
β-strand	368-374	7	31
β-strand	379-381	3	31
β-strand	401-403	3	34
β-strand	406	1	35
β-strand	410	1	35
β-strand	411-413	3	34
α-helix	414-416	3
β-strand	423	1	32
β-strand	427-432	6	34
β-strand	445-451	7	34
α-helix	453-465	13
β-strand	471-473	3	34
β-strand	483	1	36
β-strand	486	1	36
α-helix	489-495	7
β-strand	502	1	37
β-strand	507	1	38
α-helix	510-515	6
β-strand	518	1	37
α-helix	519-521	3
β-strand	524	1	39
β-strand	527-531	5	40
α-helix	544-547	4
α-helix	550-568	19
α-helix	583-596	14
α-helix	612-638	27
α-helix	657-659	3
α-helix	663-665	3
β-strand	666-667	2	40
α-helix	673-681	9
α-helix	683-689	7
α-helix	697-705	9
β-strand	711-715	5	40
α-helix	716-724	9
α-helix	727-729	3
β-strand	732-733	2	40
β-strand	740	1	40
β-strand	744	1	39
β-strand	745	1	38
β-strand	748	1	37
α-helix	757-769	13
α-helix	771-775	5
α-helix	776-780	5
α-helix	800-826	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
receptor subunit GluN1	A, C	protein	823	Xenopus laevis	A0A1L8F5J9 (AlphaFold model)
receptor subunit GluN2B	B, D	protein	824	Xenopus laevis	A7XY94 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4TLL_1 receptor subunit GluN1 (chains A, C)
ADPKIVNIGAVLSTKKHEQIFREAVNQANFFHFTRKIQLNATSVTHRPNAIQMALSVCED
LISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTV
PPYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEEKESKADKVLQFEPGT
KNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRY
APDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMEQITDPPRGCVGNTNIWKTGPLF
KRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFDGSYIIQNDRKIIW
PGGETERPQGYQMSTRLKIVTIHQEPFVYVRPTTSDGTCREEYTINGDPIKKVICNGPDE
TIPGRPTVPQCCYGFCVDLLIKLAREMDFTYEVHLVADGKFGTQERVNNSNAAAWNGMMG
ELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLW
LLVGLSVHVVAVMLYLLDRFSPFGRFEDALTLSSAMWFSWRVLLNSGLGEGAPRSFSARI
LGMVWAGFAMIIVASYTANLAAFLVLRRPEERITGINDPRLRNPSDKFIYATVKQSSVDI
YFRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGE
LFFRSGFGIGMRKDSPWKQEVSLNILKSHENGFMEELDKTWVRYQECDSRSNAPATLTFE
NMAGVFMLVAGGIVAGIFLIFIEIAYKSRAEAKRMKGLEVLFQ

Sequence of entity 2 (B, D), FASTA

>4TLL_2 receptor subunit GluN2B (chains B, D)
SRAYAQKHPNMDIAVILVGTTEEVAIKDVHEKDDFHHLPVTPRVELVTMQESDPKSIITR
ICDLMSDKKVQGVVFGDDTDQEAIAQILDFISVQTLTPILGIHGGSSMIMADKEEASMFF
QFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFENKVRSTIENSFVGWELEEVIH
LDMSLDDIDSKIQNQLCKLQSPVILLYCTKEEATYIFEVAHSVGLTGYGFTWIVPSLVAG
DTDTVPDEFPTGLISVSYDEWDYDLPARVRDGIAIITTAASTMLSEHNSIPQSKSSCNNI
QESRVYEAHMLKRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNQERKWERVGKYKDRSL
KMWPVFDLYPNSEEHKDEHLSIVTLEEAPFVIVEDVDPLSGTCMRNTVPCRKQIRPENRT
EEGGNYIKRCCKGFCIDILKKIAKTVKFTYDLYLVTNGKHGKKINGVWNGMIGEVVTKRA
YMAVGSLTINEERSEVVDFSVPFIETGISVMVSRSNGTVSPSAFLEPFSADVWVMMFVML
LIVSAVAVFVFEYFSPVGYNGPSFTIGKAIWLLWGLVFNNSLPVQNPKGTTSKIMVSVWA
FFAVIFLASYTANLAAFMIQRRYVDQVSGLSDKKFQRPNDFSPAFRFGTVPNGSTERNIR
NNYLEMHSYMVKFNQRSVQDALLSLKSGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKV
FATTGYGIAIQKDSGWKRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDID
NMAGVFYMLAAAMALSLITFIMEHLFYKSRAEAKRMKGLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4
1AC	1-aminocyclopropanecarboxylic acid	C4 H7 N O2	1
QEM	4-[(1R,2S)-3-(4-benzylpiperidin-1-yl)-1-hydroxy-2-methylpropyl]phenol	C22 H29 N O2	2
JEG	trans-1-aminocyclobutane-1,3-dicarboxylic acid	C6 H9 N O4	1

Primary citation

NMDA receptor structures reveal subunit arrangement and pore architecture. Lee, C.H., Lu, W., Michel, J.C. et al. Nature (2014) 511:191-197. DOI 10.1038/nature13548 · 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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