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- EMDB-70301: Mg2+ bound GluN1a/2B NMDAR (lower) -

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Basic information

Entry
Database: EMDB / ID: EMD-70301
TitleMg2+ bound GluN1a/2B NMDAR (lower)
Map dataLocal refinement lower Mg
Sample
  • Cell: Di-heteromeric GluN1a-2B NMDA receptor
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsMembrane Protein / Ion Channels / NMDAR
Function / homology
Function and homology information


cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / cellular response to curcumin / regulation of cAMP/PKA signal transduction / auditory behavior / pons maturation / EPHB-mediated forward signaling / positive regulation of Schwann cell migration / Assembly and cell surface presentation of NMDA receptors ...cellular response to corticosterone stimulus / cellular response to magnesium starvation / sensory organ development / cellular response to curcumin / regulation of cAMP/PKA signal transduction / auditory behavior / pons maturation / EPHB-mediated forward signaling / positive regulation of Schwann cell migration / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / response to carbohydrate / fear response / sensitization / suckling behavior / olfactory learning / response to other organism / response to methylmercury / response to hydrogen sulfide / protein localization to postsynaptic membrane / dendritic branch / conditioned taste aversion / regulation of ARF protein signal transduction / transmitter-gated monoatomic ion channel activity / response to manganese ion / apical dendrite / response to glycoside / interleukin-1 receptor binding / cellular response to dsRNA / regulation of respiratory gaseous exchange / cellular response to lipid / propylene metabolic process / response to glycine / response to growth hormone / RAF/MAP kinase cascade / positive regulation of inhibitory postsynaptic potential / heterocyclic compound binding / neuromuscular process / neurotransmitter receptor complex / negative regulation of dendritic spine maintenance / response to amine / Synaptic adhesion-like molecules / NMDA glutamate receptor activity / regulation of monoatomic cation transmembrane transport / NMDA selective glutamate receptor complex / glutamate binding / voltage-gated monoatomic cation channel activity / regulation of axonogenesis / ligand-gated sodium channel activity / response to morphine / positive regulation of glutamate secretion / calcium ion transmembrane import into cytosol / regulation of synapse assembly / startle response / male mating behavior / positive regulation of reactive oxygen species biosynthetic process / protein heterotetramerization / regulation of dendrite morphogenesis / small molecule binding / glycine binding / receptor clustering / behavioral response to pain / parallel fiber to Purkinje cell synapse / behavioral fear response / positive regulation of calcium ion transport into cytosol / social behavior / regulation of neuronal synaptic plasticity / associative learning / regulation of postsynaptic membrane potential / action potential / regulation of MAPK cascade / response to electrical stimulus / extracellularly glutamate-gated ion channel activity / multicellular organismal response to stress / neuron development / positive regulation of dendritic spine maintenance / monoatomic cation transmembrane transport / detection of mechanical stimulus involved in sensory perception of pain / cellular response to glycine / response to magnesium ion / response to mechanical stimulus / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / monoatomic cation transport / prepulse inhibition / ligand-gated monoatomic ion channel activity / calcium ion homeostasis / long-term memory / phosphatase binding / adult locomotory behavior / postsynaptic density, intracellular component / synaptic cleft / response to fungicide / monoatomic cation channel activity / cellular response to manganese ion / glutamate-gated receptor activity / regulation of long-term synaptic depression / positive regulation of synaptic transmission, glutamatergic / sensory perception of pain / response to cytokine
Similarity search - Function
Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : ...Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / : / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsSteigerwald R / Furukawa H
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH085926 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS111745 United States
CitationJournal: Nat Neurosci / Year: 2026
Title: Molecular mechanism of calcium permeability and magnesium block in NMDA receptors.
Authors: Ruben Steigerwald / Max Epstein / Tsung-Han Chou / Noriko Simorowski / Hiro Furukawa /
Abstract: Hebbian neuroplasticity, which is thought to be a cellular substrate of learning and memory, can occur by means of coincidental detection of presynaptic neurotransmitter release and Ca influx upon ...Hebbian neuroplasticity, which is thought to be a cellular substrate of learning and memory, can occur by means of coincidental detection of presynaptic neurotransmitter release and Ca influx upon postsynaptic depolarization. This is mediated at a molecular level by N-methyl-D-aspartate-type glutamate receptors, which bind glutamate and glycine and facilitate Ca influx upon relief of Mg channel block during membrane depolarization. However, the structural mechanism underlying Ca permeability and Mg blockade in N-methyl-D-aspartate-type glutamate receptors has yet to be fully elucidated. Here we demonstrate using single-particle cryo-electron microscopy that Ca permeation through the narrow constriction of the cation selectivity filter involves partial dehydration, as evidenced by several Ca binding sites. In contrast, Mg binds outside of the selectivity filter through a water network and remains hydrated, thereby acting as a channel blocker. Furthermore, the lipid network around the selectivity filter influences the stability of Mg binding in a voltage-dependent manner. Our study details the transmembrane chemistry essential for initiating neuroplasticity.
History
DepositionApr 23, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70301.png

Downloads & links

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Map

FileDownload / File: emd_70301.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal refinement lower Mg
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 400 pix.
= 342.4 Å		0.86 Å/pix.
x 400 pix.
= 342.4 Å		0.86 Å/pix.
x 400 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.3528168 - 2.1001573
Average (Standard dev.)0.0006191425 (±0.029974507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 342.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_70301_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_70301_half_map_2.map
AnnotationHalf map B
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Di-heteromeric GluN1a-2B NMDA receptor

EntireName: Di-heteromeric GluN1a-2B NMDA receptor
Components
  • Cell: Di-heteromeric GluN1a-2B NMDA receptor
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2B
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Di-heteromeric GluN1a-2B NMDA receptor

SupramoleculeName: Di-heteromeric GluN1a-2B NMDA receptor / type: cell / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Glutamate receptor ionotropic, NMDA 1

MacromoleculeName: Glutamate receptor ionotropic, NMDA 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 95.225883 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSTMHLLTFA LLFSCSFARA ASDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL QATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYN W NHIILLVS ...String:
MSTMHLLTFA LLFSCSFARA ASDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL QATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYN W NHIILLVS DDHEGRAAQK RLETLLEERE SKAEKVLQFD PGTKNVTALL MEARELEARV IILSASEDDA ATVYRAAAML DM TGSGYVW LVGEREISGN ALRYAPDGII GLQLINGKNE SAHISDAVGV VAQAVHELLE KENITDPPRG CVGNTNIWKT GPL FKRVLM SSKYADGVTG RVEFNEDGDR KFAQYSIMNL QNRKLVQVGI YNGTHVIPND RKIIWPGGET EKPRGYQMST RLKI VTIHQ EPFVYVKPTM SDGTCKEEFT VNGDPVKKVI CTGPNDTSPG SPRHTVPQCC YGFCIDLLIK LARTMQFTYE VHLVA DGKF GTQERVQNSN KKEWNGMMGE LLSGQADMIV APLTINNERA QYIEFSKPFK YQGLTILVKK EIPRSTLDSF MQPFQS TLW LLVGLSVHVV AVMLYLLDRF SPFGRFKVNS EEEEEDALTL SSAMWFSWGV LLNSGIGEGA PRSFSARILG MVWAGFA MI IVASYTANLA AFLVLDRPEE RITGINDPRL RNPSDKFIYA TVKQSSVDIY FRRQVELSTM YRHMEKHNYE SAAEAIQA V RDNKLHAFIW DSAVLEFEAS QKCDLVTTGE LFFRSGFGIG MRKDSPWKQQ VSLSILKSHE NGFMEDLDKT WVRYQECDS RSNAPATLTF ENMAGVFMLV AGGIVAGIFL IFIEIAYKRH KDANGAQ

UniProtKB: Glutamate receptor ionotropic, NMDA 1

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Macromolecule #2: Glutamate receptor ionotropic, NMDA 2B

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 96.498977 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GWSHPQFEKG GGSGGGSGGS AWSHPQFEKG ALVPRGRSQK SPPSIGIAVI LVGTSDEVAI KDAHEKDDFH HLSVVPRVEL VAMNETDPK SIITRICDLM SDRKIQGVVF ADDTDQEAIA QILDFISAQT LTPILGIHGG SSMIMADKDE SSMFFQFGPS I EQQASVML ...String:
GWSHPQFEKG GGSGGGSGGS AWSHPQFEKG ALVPRGRSQK SPPSIGIAVI LVGTSDEVAI KDAHEKDDFH HLSVVPRVEL VAMNETDPK SIITRICDLM SDRKIQGVVF ADDTDQEAIA QILDFISAQT LTPILGIHGG SSMIMADKDE SSMFFQFGPS I EQQASVML NIMEEYDWYI FSIVTTYFPG YQDFVNKIRS TIENSFVGWE LEEVLLLDMS LDDGDSKIQN QLKKLQSPII LL YCTKEEA TYIFEVANSV GLTGYGYTWI VPSLVAGDTD TVPSEFPTGL ISVSYDEWDY GLPARVRDGI AIITTAASDM LSE HSFIPE PKSSCYNTHE KRIYQSNMLN RYLINVTFEG RNLSFSEDGY QMHPKLVIIL LNKERKWERV GKWKDKSLQM KYYV WPRMC PETEEQEDDH LSIVTLEEAP FVIVESVDPL SGTCMRNTVP CQKRIISENK TDEEPGYIKK CCKGFCIDIL KKISK SVKF TYDLYLVTNG KHGKKINGTW NGMIGEVVMK RAYMAVGSLT INEERSEVVD FSVPFIETGI SVMVSRSNGT VSPSAF LEP FSADVWVMMF VMLLIVSAVA VFVFEYFSPV GYNRCLADGR EPGGPSFTIG KAIWLLWGLV FNNSVPVQNP KGTTSKI MV SVWAFFAVIF LASYTANLAA FMIQEEYVDQ VSGLSDKKFQ RPNDFSPPFR FGTVPNGSTE RNIRNNYAEM HAYMGKFN Q RGVDDALLSL KTGKLDAFIY DAAVLNYMAG RDEGCKLVTI GSGKVFASTG YGIAIQKDSG WKRQVDLAIL QLFGDGEME ELEALWLTGI CHNEKNEVMS SQLDIDNMAG VFYMLGAAMA LSLITFICEH LFYWQFRHSF MG

UniProtKB: Glutamate receptor ionotropic, NMDA 2B

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Macromolecule #3: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 3 / Number of copies: 4 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 26 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7saa

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 105462
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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