5TQ2: NMDA glutamate receptor subunit

Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A in complex with zinc at GluN1 and GluN2A. Determined by X-ray diffraction at 3.29 Å resolution. Released 14 Dec 2016.

Method: X-ray diffraction
Resolution: 3.29 Å
Organisms: Xenopus laevis, Rattus norvegicus, Mus musculus
Chains: 4
Atoms: 7,999
Mol. weight: 132.82 kDa
Ligands: ZN, NAG
Released: 14 Dec 2016

Explore 5TQ2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5TQ2 contains 45 α-helices and 83 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: 18 helices, 20 β-strands

Element	Residues	Length	Sheet
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	105-113	9
β-strand	118-120	3	1
α-helix	126-129	4
β-strand	137-139	3	1
α-helix	144-147	4
α-helix	148-157	10
β-strand	163-168	6	2
α-helix	171-185	15
β-strand	213-218	6	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	278-281	4
β-strand	288-292	5	2
α-helix	298-316	19
α-helix	324-326	3
α-helix	339-347	9
β-strand	350-351	2	3
β-strand	355	1	4
β-strand	357	1	4
β-strand	359-361	3	3
α-helix	366	1
β-strand	367-368	2	3
β-strand	372-377	6	2
β-strand	382-388	7	2
β-strand	393-395	3	2
α-helix	396	1
β-strand	400-401	2	5
β-strand	407-408	2	5

Chain B: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	6
α-helix	43-45	3
β-strand	68-73	6	6
α-helix	79-90	12
β-strand	98-101	4	6
α-helix	108-120	13
β-strand	124-128	5	6
α-helix	129-132	4
α-helix	137-139	3
β-strand	144-146	3	6
α-helix	151-164	14
β-strand	169	1	7
β-strand	170-174	5	8
α-helix	180-193	14
β-strand	199	1	7
β-strand	203-205	3	8
α-helix	211	1
α-helix	214-219	6
β-strand	226-230	5	8
α-helix	233-246	14
β-strand	254-257	4	8
α-helix	259-262	4
α-helix	273	1
β-strand	277-280	4	8
α-helix	288-305	18
α-helix	315-317	3
α-helix	335-338	4
β-strand	341-343	3	9
β-strand	346-348	3	9
β-strand	350	1	10
β-strand	356	1	10
β-strand	362-366	5	8
β-strand	372-374	3	8

Chain H: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
β-strand	10-11	2	12
β-strand	18-25	8	11
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	46-51	6	13
β-strand	58-60	3	13
α-helix	62-64	3
β-strand	68-69	2	11
β-strand	72-73	2	11
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	93-99	7	13
α-helix	100-102	3
β-strand	106-109	4	13
β-strand	113-114	2	13
β-strand	115-116	2	12
α-helix	123-125	3
β-strand	126-130	5	14
β-strand	145-151	7	14
β-strand	157	1	15
β-strand	171	1	14
α-helix	172-174	3
β-strand	175-176	2	14
β-strand	181-185	5	14
β-strand	200-202	3	16
β-strand	204	1	15
β-strand	205	1	17
β-strand	210	1	17
β-strand	213-215	3	16

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	18
β-strand	10-13	4	19
α-helix	14	1
β-strand	19-25	7	18
β-strand	33-38	6	19
β-strand	45-48	4	19
β-strand	62-67	6	18
β-strand	70-75	6	18
α-helix	80-82	3
β-strand	84-90	7	19
α-helix	96	1
β-strand	97-98	2	19
β-strand	102-106	5	19
β-strand	111	1	20
β-strand	114-118	5	21
α-helix	119-121	3
β-strand	131-139	9	21
β-strand	140	1	20
β-strand	145-150	6	22
β-strand	153-154	2	22
β-strand	159-163	5	21
α-helix	164-167	4
β-strand	173-180	8	21
α-helix	183-186	4
β-strand	192-197	6	22
β-strand	205	1	22
β-strand	208	1	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NMDA glutamate receptor subunit	A	protein	389	Xenopus laevis	A0A1L8F5J9 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2A	B	protein	360	Rattus norvegicus	Q00959 (AlphaFold model)
FAB, heavy chain	H	protein	221	Mus musculus
FAB, light chain	L	protein	214	Mus musculus

Sequence of entity 1 (A), FASTA

>5TQ2_1 NMDA glutamate receptor subunit (chains A)
PKIVNIGAVLSTKKHEQIFREAVNQANKRHFTRKIQLQATSVTHRPNAIQMALSVCEDLI
SSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVPP
YSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEGKESKSKKRNYENLDQLS
YDNKRGPKADKVLQFEPGTKNLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTG
AGYVWLVGEREISGSALRYAPDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMENIT
DPPRGCVGNTNIWKTGPLFKRVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLV
QVGIFNGSYIIQNDRKIIWPGGETEGTLV

Sequence of entity 2 (B), FASTA

>5TQ2_2 Glutamate receptor ionotropic, NMDA 2A (chains B)
LNIAVLLGHSHDVTERELRNLWGPEQATGLPLDVNVVALLMNRTDPKSLITHVCDLMSGA
RIHGLVFGDDTDQEAVAQMLDFISSQTFIPILGIHGGASMIMADKDPTSTFFQFGASIQQ
QATVMLKIMQDYDWHVFSLVTTIFPGYRDFISFIKTTVDNSFVGWDMQNVITLDTSFEDA
KTQVQLKKIHSSVILLYCSKDEAVLILSEARSLGLTGYDFFWIVPSLVSGNTELIPKEFP
SGLISVSYDDWDYSLEARVRDGLGILTTAASSMLEKFSYIPEAKASCYGQAEKPETPLHT
LHQFMVNVTWDGKDLSFTEEGYQVHPRLVVIVLNKDREWEKVGKWENQTLSLRHAVWPRY

Sequence of entity 3 (H), FASTA

>5TQ2_3 FAB, HEAVY CHAIN (chains H)
EVKLVESGPELKKPGETVKISCKASGFTFTNYGMNWVKQAPGKGLKWMGWINIYTGEPTY
ADDFKGRFAFSLETSASTAYLQINNLKNEDTATYFCARGYDYEGYFDYWGQGTTLTVSSA
KTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDL
YTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC

Sequence of entity 4 (L), FASTA

>5TQ2_4 FAB, LIGHT CHAIN (chains L)
DIVMTQAPATLSVTPGDRVSLSCRASQSIADYLYWYQQKSHESPRLLLKYASQSISGIPS
RFSGSGSGSDFTLTINSVEPEDVGMYYCQNGHSFPRTFGGGTKLEIKRADAAPTVSIFPP
SSEQLAAGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Water and common crystallization additives (SO4, GOL) are not listed.

Primary citation

Molecular Basis for Subtype Specificity and High-Affinity Zinc Inhibition in the GluN1-GluN2A NMDA Receptor Amino-Terminal Domain. Romero-Hernandez, A., Simorowski, N., Karakas, E. et al. Neuron (2016) 92:1324-1336. DOI 10.1016/j.neuron.2016.11.006 · 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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