5B3J: NMDA glutamate receptor subunit

Activation of NMDA receptors and the mechanism of inhibition by ifenprodil. Determined by X-ray diffraction at 2.9 Å resolution. Released 11 May 2016.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Xenopus laevis, Rattus norvegicus, Mus musculus
Chains: 8
Atoms: 15,954
Mol. weight: 263.8 kDa
Released: 11 May 2016

Explore 5B3J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5B3J contains 82 α-helices and 163 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: 18 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	26-33	8	1
α-helix	36-47	12
β-strand	59-66	8	1
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-85	3
β-strand	87-92	6	1
α-helix	105-111	7
β-strand	118-120	3	1
α-helix	126-129	4
β-strand	137-139	3	1
α-helix	144-147	4
α-helix	148-158	11
β-strand	163-168	6	2
α-helix	171-184	14
β-strand	213-218	6	2
α-helix	226-234	9
β-strand	239-243	5	2
α-helix	246-256	11
β-strand	267-270	4	2
α-helix	273-275	3
α-helix	278-282	5
α-helix	284	1
β-strand	288-292	5	2
α-helix	298-318	21
α-helix	323-326	4
α-helix	339-347	9
β-strand	353-354	2	3
β-strand	357-358	2	3
β-strand	360-361	2	4
β-strand	367-368	2	4
β-strand	372-378	7	2
β-strand	381-388	8	2
β-strand	393-395	3	2
α-helix	399-400	2

Chain B: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	28-33	6	5
α-helix	36-47	12
β-strand	62-66	5	5
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-85	3
β-strand	87-92	6	5
α-helix	105-111	7
β-strand	118-120	3	5
α-helix	126-129	4
β-strand	137-139	3	5
α-helix	144-147	4
α-helix	148-158	11
β-strand	163-168	6	6
α-helix	171-184	14
β-strand	213-218	6	6
α-helix	226-234	9
β-strand	239-243	5	6
α-helix	246-256	11
β-strand	267-270	4	6
α-helix	273-275	3
α-helix	278-282	5
α-helix	284	1
β-strand	288-292	5	6
α-helix	298-318	21
α-helix	322-326	5
α-helix	339-347	9
β-strand	360-361	2	7
α-helix	366	1
β-strand	367-368	2	7
β-strand	372-377	6	6
β-strand	382-388	7	6
β-strand	393-395	3	6
α-helix	399-400	2

Chain C: 13 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	32-33	2
β-strand	34-42	9	8
α-helix	47-54	8
β-strand	60	1	9
β-strand	62	1	9
β-strand	65-73	9	8
α-helix	78-91	14
β-strand	94-100	7	8
α-helix	107-119	13
β-strand	123-125	3	8
α-helix	128-131	4
β-strand	143-145	3	8
α-helix	150-164	15
β-strand	168-173	6	10
α-helix	179-191	13
β-strand	198-204	7	10
β-strand	227	1	10
β-strand	230-231	2	10
α-helix	234-241	8
β-strand	255	1	10
β-strand	257-258	2	11
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	11
α-helix	289-311	23
α-helix	315-318	4
α-helix	330-339	10
β-strand	343-344	2	12
β-strand	347-348	2	12
β-strand	351	1	13
β-strand	356	1	8
β-strand	357	1	13
β-strand	362-366	5	11
β-strand	374-380	7	11
β-strand	383-385	3	11

Chain D: 13 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	32-33	2
β-strand	34-42	9	20
α-helix	47-54	8
β-strand	60	1	21
β-strand	62	1	21
β-strand	65-73	9	20
α-helix	78-91	14
β-strand	94-100	7	20
α-helix	107-119	13
β-strand	123-125	3	20
α-helix	128-131	4
β-strand	143-145	3	20
α-helix	150-164	15
β-strand	168-173	6	22
α-helix	179-191	13
β-strand	198-204	7	22
α-helix	221-223	3
β-strand	227	1	22
β-strand	230-231	2	22
α-helix	234-241	8
β-strand	257-258	2	23
α-helix	260-263	4
β-strand	278-282	5	23
α-helix	289-311	23
α-helix	315-318	4
α-helix	331-339	9
β-strand	343-344	2	24
β-strand	347-348	2	24
β-strand	351	1	25
β-strand	356	1	20
β-strand	357	1	25
β-strand	362-367	6	23
β-strand	373-379	7	23
β-strand	384-385	2	23

Chain E: 2 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	14
β-strand	10-12	3	15
β-strand	17-24	8	14
α-helix	29-31	3
β-strand	34-40	7	15
β-strand	44-51	8	15
β-strand	58-59	2	15
β-strand	65	1	16
β-strand	68	1	16
β-strand	69-73	5	14
β-strand	78-84	7	14
β-strand	92-99	8	15
β-strand	109-112	4	15
β-strand	116-120	5	15
β-strand	126	1	17
β-strand	129-133	5	18
β-strand	144-154	11	18
β-strand	155	1	17
β-strand	160-163	4	19
β-strand	172-174	3	18
α-helix	175-177	3
β-strand	178-180	3	18
β-strand	183-193	11	18
β-strand	203-208	6	19
β-strand	213-218	6	19

Chain F: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	26
β-strand	10-14	5	27
β-strand	18-25	8	26
β-strand	33-38	6	27
β-strand	45-49	5	27
β-strand	53-54	2	27
α-helix	55	1
β-strand	62-67	6	26
β-strand	70-76	7	26
α-helix	80-82	3
β-strand	84-90	7	27
β-strand	96-97	2	27
β-strand	101-106	6	27
β-strand	110	1	28
β-strand	113-117	5	29
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	29
β-strand	139	1	28
β-strand	144-149	6	30
β-strand	152-153	2	30
β-strand	158-162	5	29
α-helix	163-166	4
β-strand	172-181	10	29
α-helix	182-186	5
β-strand	190-196	7	30
α-helix	203	1
β-strand	204-209	6	30

Chain H: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	31
β-strand	10-12	3	32
β-strand	18-24	7	31
α-helix	29-31	3
β-strand	34-40	7	32
β-strand	44-51	8	32
β-strand	58-59	2	32
β-strand	65	1	33
β-strand	68	1	33
β-strand	69-73	5	31
β-strand	78-83	6	31
β-strand	92-99	8	32
β-strand	109-112	4	32
β-strand	116-120	5	32
β-strand	126	1	34
β-strand	129-133	5	35
β-strand	144-154	11	35
β-strand	155	1	34
β-strand	160-163	4	36
α-helix	164-166	3
β-strand	172-174	3	35
α-helix	175-177	3
β-strand	178-180	3	35
β-strand	183-193	11	35
β-strand	203-208	6	36
β-strand	213-218	6	36

Chain L: 7 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	37
β-strand	10-14	5	38
β-strand	19-25	7	37
β-strand	33-38	6	38
β-strand	45-49	5	38
β-strand	53-54	2	38
α-helix	55	1
β-strand	62-67	6	37
β-strand	70-75	6	37
α-helix	80-82	3
β-strand	85-90	6	38
β-strand	96-97	2	38
β-strand	101-106	6	38
β-strand	110	1	39
β-strand	113-117	5	40
α-helix	118-120	3
α-helix	121-126	6
β-strand	128-138	11	40
β-strand	139	1	39
β-strand	143-149	7	41
β-strand	152-153	2	41
β-strand	158-162	5	40
α-helix	163-166	4
β-strand	172-181	10	40
α-helix	182-186	5
β-strand	190-197	8	41
α-helix	203	1
β-strand	204-209	6	41

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NMDA glutamate receptor subunit	A, B	protein	383	Xenopus laevis	A0A1L8F5J9 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2B	C, D	protein	364	Rattus norvegicus	Q00960 (AlphaFold model)
Fab, heavy chain	E, H	protein	224	Mus musculus
Fab, light chain	F, L	protein	213	Mus musculus

Sequence of entity 1 (A, B), FASTA

>5B3J_1 NMDA glutamate receptor subunit (chains A, B)
DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDL
ISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVP
PYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKESKSKKRNYENLDQL
SYDNKRGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMT
GAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENI
TDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKL
VQVGIFNGSYIIQNDRKIIWPGG

Sequence of entity 2 (C, D), FASTA

>5B3J_2 Glutamate receptor ionotropic, NMDA 2B (chains C, D)
SPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMS
DRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSI
EQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLD
DGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVP
SEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIY
QSNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYV
WPRM

Sequence of entity 3 (E, H), FASTA

>5B3J_3 Fab, heavy chain (chains E, H)
EVKLVESGGGLVQPGGSLKLSCAASGITFSSYSMSWVRQTPEKRLEWVAYISNGGSGTYY
PDTVKGRFTISRDNAKNSLYLQMSSLRSEDTAMYYCARPSRGGSSYWYFDVWGAGTTVTV
SSAKTTPPSVYPLAPGSAASTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQ
SDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 4 (F, L), FASTA

>5B3J_4 Fab, light chain (chains F, L)
DIQMTQSPSSLSASLGGKVTITCKASQDINKYIAWYQHKPGKGPRLLIQYTSTLQPDIPS
RFTGSGSGRDYSFSISNLEPEDIAIYYCLQYDNLYTFGGGTQLEIKRADAAPTVSIFPPS
SEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTL
TKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Primary citation

Activation of NMDA receptors and the mechanism of inhibition by ifenprodil. Tajima, N., Karakas, E., Grant, T. et al. Nature (2016) 534:63-68. DOI 10.1038/nature17679 · 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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