3QEL: NMDA glutamate receptor subunit

Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2B in complex with ifenprodil. Determined by X-ray diffraction at 2.6 Å resolution. Released 15 Jun 2011.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Xenopus laevis, Rattus norvegicus
Chains: 4
Atoms: 10,737
Mol. weight: 171.68 kDa
Ligands: NAG, QEL
Released: 15 Jun 2011

Explore 3QEL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3QEL contains 67 α-helices and 69 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: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	24	1
β-strand	25-33	9	1
α-helix	36-52	17
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	105-114	10
β-strand	118-120	3	1
α-helix	126-129	4
β-strand	137-139	3	1
α-helix	144-146	3
α-helix	147-157	11
β-strand	162-168	7	2
α-helix	171-184	14
β-strand	211-218	8	2
α-helix	226-233	8
β-strand	239-243	5	2
α-helix	246-258	13
β-strand	267-269	3	2
α-helix	273-275	3
α-helix	278-281	4
α-helix	283-284	2
β-strand	288-292	5	2
α-helix	298-316	19
α-helix	322-326	5
α-helix	339-347	9
β-strand	350-354	5	3
β-strand	357-361	5	3
β-strand	366	1	1
β-strand	367-368	2	3
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: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	34-42	9	4
α-helix	47-50	4
β-strand	65-73	9	4
α-helix	78-91	14
β-strand	94-101	8	4
α-helix	107-119	13
β-strand	123-127	5	4
α-helix	128-131	4
β-strand	143-145	3	4
α-helix	150-163	14
β-strand	168-174	7	5
α-helix	179-191	13
β-strand	198-205	8	5
α-helix	215-220	6
β-strand	227-231	5	5
α-helix	234-245	12
β-strand	255-258	4	5
α-helix	260-263	4
α-helix	274	1
β-strand	278-279	2	5
β-strand	282	1	5
α-helix	289-308	20
α-helix	327-330	4
α-helix	336-339	4
β-strand	343-344	2	6
β-strand	347-348	2	6
β-strand	351	1	7
β-strand	357	1	7
β-strand	362-367	6	5
β-strand	373-379	7	5
β-strand	384-386	3	5
α-helix	391-392	2

Chain C: 18 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	25-33	9	8
α-helix	36-52	17
β-strand	58-66	9	8
α-helix	71-77	7
α-helix	78-82	5
α-helix	83-85	3
β-strand	87-92	6	8
α-helix	105-114	10
β-strand	118-120	3	8
α-helix	126-129	4
β-strand	137-139	3	8
α-helix	144-147	4
α-helix	148-157	10
β-strand	162-168	7	9
α-helix	171-183	13
β-strand	211-218	8	9
α-helix	226-234	9
β-strand	239-243	5	9
α-helix	246-258	13
β-strand	267-270	4	9
α-helix	273-275	3
α-helix	278-282	5
α-helix	283-284	2
β-strand	288-292	5	9
α-helix	298-316	19
α-helix	324-326	3
α-helix	339-347	9
β-strand	351-354	4	10
β-strand	357-359	3	10
β-strand	360-361	2	11
β-strand	366	1	8
β-strand	367-368	2	11
β-strand	372-378	7	9
β-strand	381-388	8	9
β-strand	393-395	3	9
α-helix	399-400	2

Chain D: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	34-42	9	12
α-helix	47-50	4
β-strand	65-73	9	12
α-helix	78-89	12
β-strand	94-100	7	12
α-helix	107-119	13
β-strand	123-127	5	12
α-helix	128-131	4
β-strand	143-145	3	12
α-helix	150-163	14
β-strand	168-174	7	13
α-helix	179-192	14
β-strand	198-205	8	13
α-helix	215-220	6
β-strand	227-231	5	13
α-helix	234-246	13
β-strand	255-258	4	13
α-helix	260-263	4
α-helix	274	1
β-strand	278-282	5	13
α-helix	289-300	12
α-helix	304-311	8
α-helix	315-317	3
α-helix	336-339	4
β-strand	351	1	14
β-strand	356	1	12
β-strand	357	1	14
β-strand	362-367	6	13
β-strand	373-378	6	13
β-strand	385-386	2	13
α-helix	391-393	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NMDA glutamate receptor subunit	A, C	protein	383	Xenopus laevis	A0A1L8F5J9 (AlphaFold model)
Glutamate [NMDA] receptor subunit epsilon-2	B, D	protein	364	Rattus norvegicus	Q00960 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3QEL_1 NMDA glutamate receptor subunit (chains A, C)
DPKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDL
ISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVP
PYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKESKSKKRNYENLDQL
SYDNKRGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMT
GAGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENI
TDPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKL
VQVGIFNGSYIIQNDRKIIWPGG

Sequence of entity 2 (B, D), FASTA

>3QEL_2 Glutamate [NMDA] receptor subunit epsilon-2 (chains B, D)
SPPSIGIAVILVGTSDEVAIKDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMS
DRKIQGVVFADDTDQEAIAQILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSI
EQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLD
DGDSKIQNQLKKLQSPIILLYCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVP
SEFPTGLISVSYDEWDYGLPARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIY
QSNMLNRYLINVTFEGRDLSFSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYV
WPRM

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	6
QEL	4-[(1R,2S)-2-(4-benzylpiperidin-1-yl)-1-hydroxypropyl]phenol	C21 H27 N O2	2

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

Primary citation

Subunit arrangement and phenylethanolamine binding in GluN1/GluN2B NMDA receptors. Karakas, E., Simorowski, N., Furukawa, H. Nature (2011) 475:249-253. DOI 10.1038/nature10180 · 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…
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…
5EWJ 2.77 Å, Crystal structure of amino terminal domains of the nmda receptor subunit GLUN1 and…

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