5IPV: N-methyl-D-aspartate receptor subunit NR1-8a

Cryo-EM structure of GluN1/GluN2B NMDA receptor in the DCKA/D-APV-bound conformation, state 1. Determined by electron microscopy at 9.25 Å resolution. Released 20 Apr 2016.

Method: Electron microscopy
Resolution: 9.25 Å
Organism: Xenopus laevis
Chains: 4
Atoms: 10,209
Mol. weight: 371.77 kDa
Released: 20 Apr 2016

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

Secondary structure: helices and β-sheets

5IPV contains 122 α-helices and 132 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: 32 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	26-33	8	1
α-helix	36-51	16
β-strand	59-66	8	1
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	1
α-helix	106-114	9
β-strand	118-120	3	1
α-helix	126-128	3
β-strand	137-139	3	1
α-helix	147-158	12
β-strand	164-168	5	2
α-helix	171-186	16
β-strand	194-197	4	2
α-helix	205-213	9
β-strand	218-222	5	2
α-helix	225-237	13
β-strand	246-249	4	2
α-helix	251-254	4
α-helix	257-261	5
α-helix	262-263	2
β-strand	267-271	5	2
α-helix	277-295	19
α-helix	303-305	3
α-helix	317-326	10
β-strand	340	1	3
β-strand	346	1	3
β-strand	351-355	5	2
α-helix	357-359	3
β-strand	362-368	7	2
β-strand	371-374	4	2
α-helix	378-379	2
β-strand	397-401	5	4
β-strand	410-412	3	4
α-helix	413-414	2
β-strand	424	1	5
β-strand	430	1	5
α-helix	431-432	2
β-strand	434-439	6	4
β-strand	448-454	7	4
α-helix	456-467	12
β-strand	471-474	4	4
β-strand	484	1	6
β-strand	497	1	6
α-helix	499-505	7
β-strand	510-511	2	4
β-strand	516	1	7
α-helix	519-522	4
β-strand	526-527	2	4
α-helix	528-530	3
β-strand	533-541	9	8
α-helix	660-663	4
β-strand	671-672	2	8
α-helix	678-685	8
α-helix	690-697	8
α-helix	704-713	10
β-strand	718-722	5	8
α-helix	723-733	11
β-strand	736-747	12	8
β-strand	748	1	7
β-strand	751-752	2	4
α-helix	758-771	14
α-helix	774-782	9

Chain B: 29 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	31-37	7	9
α-helix	45-50	6
α-helix	60-61	2
β-strand	62-68	7	9
α-helix	73-87	15
β-strand	91-96	6	9
α-helix	102-114	13
β-strand	118-120	3	9
α-helix	131-133	3
β-strand	138-140	3	9
α-helix	146-158	13
β-strand	163-169	7	10
α-helix	177-187	11
β-strand	193-200	8	10
α-helix	210-215	6
β-strand	222-226	5	10
α-helix	229-242	14
β-strand	250-253	4	10
α-helix	255-258	4
α-helix	269	1
β-strand	273-277	5	10
α-helix	284-306	23
α-helix	319-321	3
α-helix	327-334	8
β-strand	338-339	2	11
β-strand	342-343	2	11
β-strand	346	1	12
β-strand	351	1	9
β-strand	352	1	12
β-strand	356-362	7	10
β-strand	368-375	8	10
β-strand	378-381	4	10
β-strand	401-403	3	13
β-strand	411-413	3	13
α-helix	414-416	3
β-strand	427-430	4	13
β-strand	447-451	5	13
α-helix	453-465	13
β-strand	471-473	3	13
β-strand	481-483	3	14
β-strand	486-488	3	14
α-helix	490-495	6
β-strand	501-502	2	13
α-helix	510-515	6
α-helix	519-521	3
β-strand	525	1	15
β-strand	527-531	5	16
α-helix	663-664	2
β-strand	666-667	2	16
α-helix	673-681	9
α-helix	683-689	7
α-helix	690-692	3
α-helix	697-705	9
β-strand	711-715	5	16
α-helix	716-724	9
β-strand	732-733	2	16
α-helix	738-739	2
β-strand	743	1	15
α-helix	757-768	12
α-helix	771-775	5
α-helix	776-780	5

Chain C: 32 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	26-33	8	17
α-helix	36-51	16
β-strand	59-66	8	17
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	17
α-helix	106-114	9
β-strand	118-120	3	17
α-helix	126-128	3
β-strand	137-139	3	17
α-helix	147-158	12
β-strand	164-168	5	18
α-helix	171-186	16
β-strand	194-197	4	18
α-helix	205-213	9
β-strand	218-222	5	18
α-helix	225-237	13
β-strand	246-249	4	18
α-helix	251-254	4
α-helix	257-261	5
α-helix	262-263	2
β-strand	267-271	5	18
α-helix	277-295	19
α-helix	303-305	3
α-helix	317-326	10
β-strand	340	1	19
β-strand	346	1	19
β-strand	350-355	6	18
α-helix	357-359	3
β-strand	362-368	7	18
β-strand	371-374	4	18
α-helix	378-379	2
β-strand	397-401	5	20
β-strand	410-412	3	20
α-helix	413-414	2
β-strand	424	1	21
β-strand	430	1	21
α-helix	431-432	2
β-strand	434-439	6	20
β-strand	448-454	7	20
α-helix	456-467	12
β-strand	471-474	4	20
β-strand	484	1	22
β-strand	488	1	23
β-strand	493	1	23
β-strand	497	1	22
α-helix	499-505	7
β-strand	510-511	2	20
β-strand	516	1	24
α-helix	519-522	4
β-strand	526-527	2	20
α-helix	528-530	3
β-strand	533-541	9	25
α-helix	660-663	4
β-strand	671-672	2	25
α-helix	678-685	8
α-helix	690-697	8
α-helix	704-713	10
β-strand	718-722	5	25
α-helix	723-733	11
β-strand	736-747	12	25
β-strand	748	1	24
β-strand	751-752	2	20
α-helix	758-771	14
α-helix	774-782	9

Chain D: 29 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	31-37	7	26
α-helix	45-50	6
α-helix	60-61	2
β-strand	62-68	7	26
α-helix	73-87	15
β-strand	91-96	6	26
α-helix	102-114	13
β-strand	118-120	3	26
α-helix	123-126	4
α-helix	131-133	3
β-strand	138-140	3	26
α-helix	146-158	13
β-strand	163-169	7	27
α-helix	177-187	11
β-strand	193-200	8	27
α-helix	210-215	6
β-strand	222-226	5	27
α-helix	229-242	14
β-strand	250-253	4	27
α-helix	255-258	4
α-helix	269	1
β-strand	273-276	4	27
α-helix	284-306	23
α-helix	319-321	3
α-helix	327-334	8
β-strand	338-339	2	28
β-strand	342-343	2	28
β-strand	346	1	29
β-strand	351	1	26
β-strand	352	1	29
β-strand	357-362	6	27
β-strand	368-375	8	27
β-strand	378-381	4	27
β-strand	401-403	3	30
β-strand	411-413	3	30
α-helix	414-416	3
β-strand	427-430	4	30
β-strand	447-451	5	30
α-helix	453-465	13
β-strand	471-473	3	30
β-strand	481-483	3	31
β-strand	486-488	3	31
α-helix	490-495	6
β-strand	501-502	2	30
α-helix	510-515	6
α-helix	519-521	3
β-strand	525	1	32
β-strand	527-531	5	33
α-helix	663-664	2
β-strand	666-667	2	33
α-helix	673-681	9
α-helix	683-689	7
α-helix	690-692	3
α-helix	697-705	9
β-strand	711-715	5	33
α-helix	716-724	9
β-strand	732-733	2	33
β-strand	743	1	32
α-helix	757-768	12
α-helix	771-775	5
α-helix	776-780	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
N-methyl-D-aspartate receptor subunit NR1-8a	A, C	protein	822	Xenopus laevis	A0A1L8F5J9 (AlphaFold model)
Ionotropic glutamate receptor subunit NR2B	B, D	protein	825	Xenopus laevis	A7XY94 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5IPV_1 N-methyl-D-aspartate receptor subunit NR1-8a (chains A, C)
DPKIVNIGAVLSTKKHEQIFREAVNQANFFHFTRKIQLNATSVTHRPNAIQMALSVCEDL
ISSQVYAILVSHPPAPTDHLTPTPISYTAGFYRIPVIGLTTRMSIYSDKSIHLSFLRTVP
PYSHQALVWFEMMRLFNWNHVILIVSDDHEGRAAQKKLETLLEEKESKADKVLQFEPGTK
NLTALLLEAKELEARVIILSASEDDATAVYKSAAMLDMTGAGYVWLVGEREISGSALRYA
PDGIIGLQLINGKNESAHISDAVAVVAQAIHELFEMEQITDPPRGCVGNTNIWKTGPLFK
RVLMSSKYPDGVTGRIEFNEDGDRKFAQYSIMNLQNRKLVQVGIFDGSYIIQNDRKIIWP
GGETERPQGYQMSTRLKIVTIHQEPFVYVRPTTSDGTCREEYTINGDPIKKVICNGPDET
IPGRPTVPQCCYGFCVDLLIKLAREMDFTYEVHLVADGKFGTQERVNNSNAAAWNGMMGE
LLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTILVKKEIPRSTLDSFMQPFQSTLWL
LVGLSVHVVAVMLYLLDRFSPFGRFEDALTLSSAMWFSWRVLLNSGLGEGAPRSFSARIL
GMVWAGFAMIIVASYTANLAAFLVLRRPEERITGINDPRLRNPSDKFIYATVKQSSVDIY
FRRQVELSTMYRHMEKHNYESAAEAIQAVRDNKLHAFIWDSAVLEFEASQKCDLVTTGEL
FFRSGFGIGMRKDSPWKQEVSLNILKSHENGFMEELDKTWVRYQECDSRSNAPATLTFEN
MAGVFMLVAGGIVAGIFLIFIEIAYKSRAEAKRMKGLEVLFQ

Sequence of entity 2 (B, D), FASTA

>5IPV_2 Ionotropic glutamate receptor subunit NR2B (chains B, D)
MRPTEACCYLKISLIILFYSRAYAQKHPNMDIAVILVGTTEEVAIKDVHEKDDFHHLPVT
PRVELVTMQESDPKSIITRICDLMSDKKVQGVVFGDDTDQEAIAQILDFISVQTLTPILG
IHGGSSMIMADKEEASMFFQFGPSIEQQASVMLNIMEEYDWYIFSIVTTYFPGYQDFENK
VRSTIENSFVGWELEEVIHLDMSLDDIDSKIQNQLKKLQSPVILLYCTKEEATYIFEVAH
SVGLTGYGFTWIVPSLVAGDTDTVPDEFPTGLISVSYDEWDYDLPARVRDGIAIITTAAS
TMLSEHNSIPQSKSSCNNIQESRVYEAHMLKRYLINVTFEGRDLSFSEDGYQMHPKLVII
LLNQERKWERVGKYKDRSLKMWPVFDLYPNSEEHKDEHLSIVTLEEAPFVIVEDVDPLSG
TCMRNTVPCRKQIRPENRTEEGGNYIKRCCKGFCIDILKKIAKTVKFTYDLYLVTNGKHG
KKINGVWNGMIGEVVTKRAYMAVGSLTINEERSEVVDFSVPFIETGISVMVSRSNGTVSP
SAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNGPSFTIGKAIWLLWGLVFNNS
LPVQNPKGTTSKIMVSVWAFFAVIFLASYTANLAAFMIQRRYVDQVSGLSDKKFQRPNDF
SPAFRFGTVPNGSTERNIRNNYLEMHSYMVKFNQRSVQDALLSLKSGKLDAFIYDAAVLN
YMAGRDEGCKLVTIGSGKVFATTGYGIAIQKDSGWKRQVDLAILQLFGDGEMEELEALWL
TGICHNEKNEVMSSQLDIDNMAGVFYMLAAAMALSLITFIMEHLF

Primary citation

Mechanism of NMDA Receptor Inhibition and Activation. Zhu, S., Stein, R.A., Yoshioka, C. et al. Cell (2016) 165:704-714. DOI 10.1016/j.cell.2016.03.028 · 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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