9OBT: TMD of glutamate/glycine-bound GluN1a/2B NMDAR

TMD of glutamate/glycine-bound GluN1a/2B NMDAR. Determined by electron microscopy at 3.01 Å resolution. Released 6 May 2026.

Method: Electron microscopy
Resolution: 3.01 Å
Organism: Rattus norvegicus
Chains: 4
Atoms: 3,954
Mol. weight: 387.26 kDa
Ligands: POV, CLR
Released: 6 May 2026

Explore 9OBT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9OBT contains 20 α-helices and 8 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.

Chains A and C: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	558	1	1
α-helix	560-582	23
α-helix	603-614	12
α-helix	627-656	30
β-strand	808	1	2
α-helix	810-839	30

Chains B and D: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	549-551	3
β-strand	554	1	3
α-helix	556-578	23
α-helix	602-613	12
α-helix	627-655	29
β-strand	813	1	1
α-helix	817-819	3
α-helix	820-840	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutamate receptor ionotropic, NMDA 1	A, C	protein	847	Rattus norvegicus	P35439 (AlphaFold model)
Glutamate receptor ionotropic, NMDA 2B	B, D	protein	862	Rattus norvegicus	Q00960 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9OBT_1 Glutamate receptor ionotropic, NMDA 1 (chains A, C)
MSTMHLLTFALLFSCSFARAASDPKIVNIGAVLSTRKHEQMFREAVNQANKRHGSWKIQL
QATSVTHKPNAIQMALSVCEDLISSQVYAILVSHPPTPNDHFTPTPVSYTAGFYRIPVLG
LTTRMSIYSDKSIHLSFLRTVPPYSHQSSVWFEMMRVYNWNHIILLVSDDHEGRAAQKRL
ETLLEERESKAEKVLQFDPGTKNVTALLMEARELEARVIILSASEDDAATVYRAAAMLDM
TGSGYVWLVGEREISGNALRYAPDGIIGLQLINGKNESAHISDAVGVVAQAVHELLEKEN
ITDPPRGCVGNTNIWKTGPLFKRVLMSSKYADGVTGRVEFNEDGDRKFAQYSIMNLQNRK
LVQVGIYNGTHVIPNDRKIIWPGGETEKPRGYQMSTRLKIVTIHQEPFVYVKPTMSDGTC
KEEFTVNGDPVKKVICTGPNDTSPGSPRHTVPQCCYGFCIDLLIKLARTMQFTYEVHLVA
DGKFGTQERVQNSNKKEWNGMMGELLSGQADMIVAPLTINNERAQYIEFSKPFKYQGLTI
LVKKEIPRSTLDSFMQPFQSTLWLLVGLSVHVVAVMLYLLDRFSPFGRFKVNSEEEEEDA
LTLSSAMWFSWGVLLNSGIGEGAPRSFSARILGMVWAGFAMIIVASYTANLAAFLVLDRP
EERITGINDPRLRNPSDKFIYATVKQSSVDIYFRRQVELSTMYRHMEKHNYESAAEAIQA
VRDNKLHAFIWDSAVLEFEASQKCDLVTTGELFFRSGFGIGMRKDSPWKQQVSLSILKSH
ENGFMEDLDKTWVRYQECDSRSNAPATLTFENMAGVFMLVAGGIVAGIFLIFIEIAYKRH
KDANGAQ

Sequence of entity 2 (B, D), FASTA

>9OBT_2 Glutamate receptor ionotropic, NMDA 2B (chains B, D)
GWSHPQFEKGGGSGGGSGGSAWSHPQFEKGALVPRGRSQKSPPSIGIAVILVGTSDEVAI
KDAHEKDDFHHLSVVPRVELVAMNETDPKSIITRICDLMSDRKIQGVVFADDTDQEAIAQ
ILDFISAQTLTPILGIHGGSSMIMADKDESSMFFQFGPSIEQQASVMLNIMEEYDWYIFS
IVTTYFPGYQDFVNKIRSTIENSFVGWELEEVLLLDMSLDDGDSKIQNQLKKLQSPIILL
YCTKEEATYIFEVANSVGLTGYGYTWIVPSLVAGDTDTVPSEFPTGLISVSYDEWDYGLP
ARVRDGIAIITTAASDMLSEHSFIPEPKSSCYNTHEKRIYQSNMLNRYLINVTFEGRNLS
FSEDGYQMHPKLVIILLNKERKWERVGKWKDKSLQMKYYVWPRMCPETEEQEDDHLSIVT
LEEAPFVIVESVDPLSGTCMRNTVPCQKRIISENKTDEEPGYIKKCCKGFCIDILKKISK
SVKFTYDLYLVTNGKHGKKINGTWNGMIGEVVMKRAYMAVGSLTINEERSEVVDFSVPFI
ETGISVMVSRSNGTVSPSAFLEPFSADVWVMMFVMLLIVSAVAVFVFEYFSPVGYNRCLA
DGREPGGPSFTIGKAIWLLWGLVFNNSVPVQNPKGTTSKIMVSVWAFFAVIFLASYTANL
AAFMIQEEYVDQVSGLSDKKFQRPNDFSPPFRFGTVPNGSTERNIRNNYAEMHAYMGKFN
QRGVDDALLSLKTGKLDAFIYDAAVLNYMAGRDEGCKLVTIGSGKVFASTGYGIAIQKDS
GWKRQVDLAILQLFGDGEMEELEALWLTGICHNEKNEVMSSQLDIDNMAGVFYMLGAAMA
LSLITFICEHLFYWQFRHSFMG

Ligands and cofactors

ID	Name	Formula	Copies
POV	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl…	C42 H82 N O8 P	4
CLR	Cholesterol	C27 H46 O	2

Primary citation

Molecular mechanism of calcium permeability and magnesium block in NMDA receptors. Steigerwald, R., Epstein, M., Chou, T.H. et al. Nat Neurosci (2026) 29:1293-1302. DOI 10.1038/s41593-026-02283-3 · PubMed

Other PDB entries of the same protein (UniProt P35439 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1PB7 1.35 Å, Crystal structure of the NR1 ligand binding core in complex with glycine at 1.35 Å…
1Y20 1.4 Å, Crystal structure of the NR1 ligand-binding core in complex with ACPC
1PB8 1.45 Å, Crystal structure of the NR1 ligand binding core in complex with D-serine at 1.45 Å…
1Y1Z 1.5 Å, Crystal structure of the NR1 ligand binding core in complex with ACBC
5U8C 1.6 Å, Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and…
1PB9 1.6 Å, Crystal structure of the NR1 ligand binding core in complex with D-cycloserine at 1.60 Å…
6UZ6 1.66 Å, Crystal structure of GLUN1/GLUN2A-4M mutant ligand-binding domain in complex with…
5I57 1.7 Å, Glutamate- and glycine-bound GluN1/GluN2A agonist binding domains
9NYZ 1.71 Å, Crystal structure of DCKA/glutamate-bound GluN1/GluN2A agonist binding domains with…
1Y1M 1.8 Å, Crystal structure of the NR1 ligand binding core in complex with cycloleucine
4NF8 1.86 Å, Crystal structure of GluN1/GluN2A ligand-binding domain in complex with glycine and…
6UZR 1.87 Å, Crystal structure of GLUN1/GLUN2A ligand-binding domain in complex with glycine and…

Browse structure collections

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