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- EMDB-70433: GluN1/GluN3A in complex with CGP and DCKA, LBD-focused, in antago... -

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Basic information

Entry
Database: EMDB / ID: EMD-70433
TitleGluN1/GluN3A in complex with CGP and DCKA, LBD-focused, in antagonist-bound conformation
Map dataGluN1/GluN3A in complex with CGP and DCKA, LBD-focused, in antagonist-bound conformation
Sample
  • Complex: di-heteromeric GluN1/GluN3A in complex with CGP and DCKA, LBD-focused, in antagonist-bound conformation
    • 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


serine binding / negative regulation of dendritic spine 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 ...serine binding / negative regulation of dendritic spine 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 / response to glycoside / transmitter-gated monoatomic ion channel activity / regulation of respiratory gaseous exchange / propylene metabolic process / response to glycine / RAF/MAP kinase cascade / glutamate receptor activity / neuromuscular process / neurotransmitter receptor complex / response to amine / Synaptic adhesion-like molecules / NMDA glutamate receptor activity / regulation of monoatomic cation transmembrane transport / NMDA selective glutamate receptor complex / glutamate binding / regulation of axonogenesis / ligand-gated sodium channel activity / startle response / voltage-gated monoatomic cation channel activity / response to morphine / calcium ion transmembrane import into cytosol / regulation of synapse assembly / positive regulation of reactive oxygen species biosynthetic process / male mating behavior / protein heterotetramerization / dendrite development / regulation of dendrite morphogenesis / glycine binding / positive regulation of calcium ion transport into cytosol / parallel fiber to Purkinje cell synapse / social behavior / regulation of neuronal synaptic plasticity / associative learning / neuron development / positive regulation of dendritic spine maintenance / monoatomic cation transmembrane transport / cellular response to glycine / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / monoatomic cation transport / ligand-gated monoatomic ion channel activity / prepulse inhibition / phosphatase binding / long-term memory / adult locomotory behavior / regulation of long-term neuronal synaptic plasticity / calcium ion homeostasis / response to fungicide / monoatomic cation channel activity / sensory perception of pain / glutamate-gated receptor activity / cellular response to manganese ion / response to amphetamine / positive regulation of synaptic transmission, glutamatergic / glutamate-gated calcium ion channel activity / presynaptic modulation of chemical synaptic transmission / presynaptic active zone membrane / visual learning / synaptic cleft / regulation of neuron apoptotic process / ionotropic glutamate receptor signaling pathway / learning / protein phosphatase 2A binding / excitatory synapse / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / excitatory postsynaptic potential / positive regulation of excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / synaptic membrane / sodium ion transmembrane transport / synaptic transmission, glutamatergic / memory / cerebral cortex development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / response to calcium ion / regulation of synaptic plasticity / regulation of membrane potential / postsynaptic density membrane / intracellular calcium ion homeostasis / modulation of chemical synaptic transmission / calcium ion transmembrane transport / calcium channel activity / calcium ion transport / terminal bouton / synaptic vesicle membrane / rhythmic process / synaptic vesicle
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: 3.41 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: To Be Published
Title: GluN1/GluN3A in complex with CGP and DCKA, LBD-focused, in antagonist-bound conformation
Authors: Kim J / Gouaux E
History
DepositionApr 29, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70433.png

Downloads & links

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Map

FileDownload / File: emd_70433.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, LBD-focused, in antagonist-bound conformation
Projections & slices

Image control

Size
Brightness
Contrast
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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8442 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.65497375 - 1.046488
Average (Standard dev.)0.0007744425 (±0.02036812)
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: unsharp map

Fileemd_70433_additional_1.map
Annotationunsharp map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_70433_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_70433_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : di-heteromeric GluN1/GluN3A in complex with CGP and DCKA, LBD-foc...

EntireName: di-heteromeric GluN1/GluN3A in complex with CGP and DCKA, LBD-focused, in antagonist-bound conformation
Components
  • Complex: di-heteromeric GluN1/GluN3A in complex with CGP and DCKA, LBD-focused, in antagonist-bound conformation
    • 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 in complex with CGP and DCKA, LBD-foc...

SupramoleculeName: di-heteromeric GluN1/GluN3A in complex with CGP and DCKA, LBD-focused, in antagonist-bound conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 290 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.41 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 80690
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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