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- EMDB-70399: GluN1/GluN3A in complex with CGP and DCKA -

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Basic information

Entry
Database: EMDB / ID: EMD-70399
TitleGluN1/GluN3A in complex with CGP and DCKA
Map dataGluN1/GluN3A in complex with CGP and DCKA
Sample
  • Complex: Di-heteromeric GluN1/GluN3A NMDA receptor in complex with CGP and DCKA
    • Protein or peptide: Isoform E of Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 3A
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: [(1S)-1-[[7-bromanyl-2,3-bis(oxidanylidene)-1,4-dihydroquinoxalin-5-yl]methylamino]ethyl]phosphonic acid
Keywordsligand-gated ion channel / NMDA / inhibitor / TRANSPORT PROTEIN
Function / homology
Function and homology information


negative regulation of dendritic spine development / serine binding / mesencephalic trigeminal nucleus development / trigeminal motor nucleus development / pons maturation / EPHB-mediated forward signaling / positive regulation of Schwann cell migration / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / protein localization to postsynaptic membrane ...negative regulation of dendritic spine development / serine binding / mesencephalic trigeminal nucleus development / trigeminal motor nucleus development / pons maturation / EPHB-mediated forward signaling / positive regulation of Schwann cell migration / Assembly and cell surface presentation of NMDA receptors / regulation of cell communication / protein localization to postsynaptic membrane / conditioned taste aversion / suckling behavior / olfactory learning / dendritic branch / positive regulation of mitochondrial calcium ion concentration / response to glycoside / transmitter-gated monoatomic ion channel activity / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / neurotransmitter receptor complex / RAF/MAP kinase cascade / response to amine / Synaptic adhesion-like molecules / negative regulation of dendritic spine maintenance / glutamate receptor activity / NMDA glutamate receptor activity / regulation of monoatomic cation transmembrane transport / neuromuscular process / NMDA selective glutamate receptor complex / glutamate binding / regulation of axonogenesis / ligand-gated sodium channel activity / startle response / voltage-gated monoatomic cation channel activity / regulation of synapse assembly / calcium ion transmembrane import into cytosol / response to morphine / positive regulation of reactive oxygen species biosynthetic process / male mating behavior / protein heterotetramerization / regulation of dendrite morphogenesis / dendrite development / glycine binding / parallel fiber to Purkinje cell synapse / positive regulation of calcium ion transport into cytosol / associative learning / hypothalamus development / regulation of neuronal synaptic plasticity / social behavior / monoatomic cation transmembrane transport / positive regulation of dendritic spine maintenance / cellular response to glycine / Unblocking of NMDA receptors, glutamate binding and activation / response to fungicide / monoatomic cation transport / calcium ion homeostasis / glutamate receptor binding / prepulse inhibition / phosphatase binding / long-term memory / adult locomotory behavior / regulation of long-term neuronal synaptic plasticity / monoatomic cation channel activity / response to amphetamine / glutamate-gated receptor activity / sensory perception of pain / cellular response to manganese ion / positive regulation of synaptic transmission, glutamatergic / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / visual learning / hippocampus development / synaptic cleft / presynaptic modulation of chemical synaptic transmission / regulation of neuron apoptotic process / ionotropic glutamate receptor signaling pathway / excitatory synapse / protein phosphatase 2A binding / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / learning / dendrite membrane / excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / positive regulation of excitatory postsynaptic potential / brain development / sodium ion transmembrane transport / synaptic membrane / synaptic transmission, glutamatergic / cerebral cortex development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / memory / response to calcium ion / regulation of synaptic plasticity / postsynaptic density membrane / modulation of chemical synaptic transmission / intracellular calcium ion homeostasis / calcium channel activity / calcium ion transmembrane transport
Similarity search - Function
: / : / 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. ...: / : / 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 3A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.67 Å
AuthorsKim J / Gouaux E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) United States
CitationJournal: Nat Struct Mol Biol / Year: 2026
Title: Structural and mechanistic insights into gating and allosteric modulation of GluN1-GluN3A NMDA receptors.
Authors: Junhoe Kim / Avery J Benton / James S Lotti / Nirvan Rouzbeh / Kasper B Hansen / Eric Gouaux /
Abstract: N-methyl-D-aspartate receptors (NMDARs) mediate excitatory signaling essential for synaptic plasticity and memory. Unlike GluN2-containing NMDARs, GluN3-containing receptors are activated solely by ...N-methyl-D-aspartate receptors (NMDARs) mediate excitatory signaling essential for synaptic plasticity and memory. Unlike GluN2-containing NMDARs, GluN3-containing receptors are activated solely by glycine and exhibit profound desensitization and paradoxical potentiation by GluN1-selective antagonists, including CGP-78608 (CGP). Although GluN3A-containing NMDARs regulate synapse pruning and excitotoxicity, and are associated with schizophrenia, autism and stroke, their native stoichiometry and gating mechanism are poorly defined. Here, using single-molecule pull-down analysis, we show that native GluN3A-containing receptors are diheteromeric assemblies. Cryogenic-electron microscopy analysis of GluN1-GluN3A receptors in antagonist-bound, preactive, active and desensitized states, augmented by electrophysiology and pharmacology experiments, show how glycine activates the receptor solely via GluN3A-dependent conformational changes, opening the gate with two-fold symmetry, and induces a roughly four-fold symmetric desensitized state. CGP-bound GluN1 restricts GluN3A rotation, promoting glycine-induced activation by blocking desensitization. These findings illuminate how CGP potentiates GluN1-GluN3A receptor activity, place the receptor gating mechanism on a structural foundation and define the molecular basis for pharmacological modulation.
History
DepositionApr 28, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateOct 14, 2026-
Current statusOct 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70399.png

Downloads & links

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Map

FileDownload / File: emd_70399.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGluN1/GluN3A in complex with CGP and DCKA
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 480 pix.
= 405.216 Å		0.84 Å/pix.
x 480 pix.
= 405.216 Å		0.84 Å/pix.
x 480 pix.
= 405.216 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8442 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.4952518 - 0.87331426
Average (Standard dev.)0.00077720697 (±0.017434942)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 405.216 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: LBD-TMD unsharp map

Fileemd_70399_additional_1.map
AnnotationLBD-TMD unsharp map
Projections & Slices
AxesZYX

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Additional map: TMD-focused refined map

Fileemd_70399_additional_2.map
AnnotationTMD-focused refined map
Projections & Slices
AxesZYX

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Additional map: LBD-focused refined map

Fileemd_70399_additional_3.map
AnnotationLBD-focused refined map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_70399_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_70399_half_map_2.map
AnnotationHalf Map B
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Sample components

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Entire : Di-heteromeric GluN1/GluN3A NMDA receptor in complex with CGP and DCKA

EntireName: Di-heteromeric GluN1/GluN3A NMDA receptor in complex with CGP and DCKA
Components
  • Complex: Di-heteromeric GluN1/GluN3A NMDA receptor in complex with CGP and DCKA
    • Protein or peptide: Isoform E of Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 3A
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: [(1S)-1-[[7-bromanyl-2,3-bis(oxidanylidene)-1,4-dihydroquinoxalin-5-yl]methylamino]ethyl]phosphonic acid

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Supramolecule #1: Di-heteromeric GluN1/GluN3A NMDA receptor in complex with CGP and DCKA

SupramoleculeName: Di-heteromeric GluN1/GluN3A NMDA receptor in complex with CGP and DCKA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 411 KDa

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Macromolecule #1: Isoform E of Glutamate receptor ionotropic, NMDA 1

MacromoleculeName: Isoform E of 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: 97.873969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSTMHLLTFA LLFSCSFARA ACDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYN W NHIILLVS ...String:
MSTMHLLTFA LLFSCSFARA ACDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYN W NHIILLVS DDHEGRAAQK RLETLLEERE SKAEKVLQFD PGTKNVTALL MEARELEARV IILSASEDDA ATVYRAAAML NM TGSGYVW LVGEREISGN ALRYAPDGII GLQLINGKNE SAHISDAVGV VAQAVHELLE KENITDPPRG CVGNTNIWKT GPL FKRVLM SSKYADGVTG RVEFNEDGDR KFANYSIMNL QNRKLVQVGI YNGTHVIPND RKIIWPGGET EKPRGYQMST RLKI VTIHQ EPFVYVKPTM SDGTCKEEFT VNGDPVKKVI CTGPNDTSPG SPRHTVPQCC YGFCIDLLIK LARTMNFTYE VHLVA DGKF GTQERVNNSN 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 MRKDSPWKQN VSLSILKSHE NGFMEDLDKT WVRYQECDS RSNAPATLTF ENMAGVFMLV AGGIVAGIFL IFIEIAYKRH KDARRKQLVP RGSAAAASGL RSHHHHHHHH

UniProtKB: Glutamate receptor ionotropic, NMDA 1

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Macromolecule #2: Glutamate receptor ionotropic, NMDA 3A

MacromoleculeName: Glutamate receptor ionotropic, NMDA 3A / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 108.280352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRRLSLWWLL SRVCLLLPPP CALVLAGVPS SSSHPQPCQI LKRIGHAVRV GAVHLQPWTT APRAASRAQE GGRAGAQRDD PESGTWRPP APSQGARWLG SALHGRGPPG SRKLGEGAGA ETLWPRDALL FAVENLNRVE GLLPYNLSLE VVMAIEAGLG D LPLMPFSS ...String:
MRRLSLWWLL SRVCLLLPPP CALVLAGVPS SSSHPQPCQI LKRIGHAVRV GAVHLQPWTT APRAASRAQE GGRAGAQRDD PESGTWRPP APSQGARWLG SALHGRGPPG SRKLGEGAGA ETLWPRDALL FAVENLNRVE GLLPYNLSLE VVMAIEAGLG D LPLMPFSS PSSPWSSDPF SFLQSVCHTV VVQGVSALLA FPQSQGEMME LDLVSSVLHI PVLSIVRHEF PRESQNPLHL QL SLENSLS SDADVTVSIL TMNNWYNFSL LLCQEDWNIT DFLLLTENNS KFHLESVINI TANLSSTKDL LSFLQVQMDN IRN STPTMV MFGCDMDSIR QIFEMSTQFG LSPPELHWVL GDSQNVEELR TEGLPLGLIA HGKTTQSVFE YYVQDAMELV ARAV ATATM IQPELALLPS TMNCMDVKTT NLTSGQYLSR FLANTTFRGL SGSIKVKGST IISSENNFFI WNLQHDPMGK PMWTR LGSW QGGRIVMDSG IWPEQAQRHK THFQHPNKLH LRVVTLIEHP FVFTREVDDE GLCPAGQLCL DPMTNDSSML DRLFSS LHS SNDTVPIKFK KCCYGYCIDL LEQLAEDMNF DFDLYIVGDG KYGAWKNGHW TGLVGDLLSG TANMAVTSFS INTARSQ VI DFTSPFFSTS LGILVRTRDT AAPIGAFMWP LHWTMWLGIF VALHITAIFL TLYEWKSPFG MTPKGRNRNK VFSFSSAL N VCYALLFGRT AAIKPPKCWT GRFLMNLWAI FCMFCLSTYT ANLAAVMVGE KIYEELSGIH DPKLHHPSQG FRFGTVRES SAEDYVRQSF PEMHEYMRRY NVPATPDGVQ YLKNDPEKLD AFIMDKALLD YEVSIDADCK LLTVGKPFAI EGYGIGLPPN SPLTSNISE LISQYKSHGF MDVLHDKWYK VVPCGKRSFA VTETLQMGIK HFSGLFVLLC IGFGLSILTT IGEHIVHRLL L PRIKNKSK LQ

UniProtKB: Glutamate receptor ionotropic, NMDA 3A

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: [(1S)-1-[[7-bromanyl-2,3-bis(oxidanylidene)-1,4-dihydroquinoxalin...

MacromoleculeName: [(1S)-1-[[7-bromanyl-2,3-bis(oxidanylidene)-1,4-dihydroquinoxalin-5-yl]methylamino]ethyl]phosphonic acid
type: ligand / ID: 5 / Number of copies: 2 / Formula: J86
Molecular weightTheoretical: 378.116 Da
Chemical component information

ChemComp-J86:
[(1S)-1-[[7-bromanyl-2,3-bis(oxidanylidene)-1,4-dihydroquinoxalin-5-yl]methylamino]ethyl]phosphonic acid

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 290 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Number real images: 14481 / Average electron dose: 50.0 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: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: Ab initio model from 2D class average
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.67 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.0) / Number images used: 80690
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.0)
FSC plot (resolution estimation)

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