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- EMDB-38847: GluN1b-GluN2D NMDA receptor in complex with competitive antagonis... -

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Basic information

Entry
Database: EMDB / ID: EMD-38847
TitleGluN1b-GluN2D NMDA receptor in complex with competitive antagonist R-CPP and allosteric inhibitor YY-23
Map data
Sample
  • Complex: N-methyl-D-aspartate receptors
    • Protein or peptide: Isoform 6 of Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2D
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(2~{S})-2-methyl-4-[(1~{R},2~{R},4~{S},6~{S},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S},18~{R})-7,9,13,18-tetramethyl-16-oxidanyl-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-yl]butoxy]oxane-3,4,5-triol
Keywordsion channel / calcium permeable / glutamate receptor / neuronal expression / MEMBRANE PROTEIN / MEMBRANE PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


regulation of sensory perception of pain / glycine-gated cation channel activity / excitatory chemical synaptic transmission / Synaptic adhesion-like molecules / response to glycine / propylene metabolic process / cellular response to L-glutamate / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity ...regulation of sensory perception of pain / glycine-gated cation channel activity / excitatory chemical synaptic transmission / Synaptic adhesion-like molecules / response to glycine / propylene metabolic process / cellular response to L-glutamate / Assembly and cell surface presentation of NMDA receptors / regulation of monoatomic cation transmembrane transport / NMDA glutamate receptor activity / voltage-gated monoatomic cation channel activity / NMDA selective glutamate receptor complex / Neurexins and neuroligins / glutamate binding / ligand-gated sodium channel activity / neurotransmitter receptor complex / calcium ion transmembrane import into cytosol / protein heterotetramerization / glycine binding / startle response / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of calcium ion transport into cytosol / Long-term potentiation / excitatory synapse / monoatomic cation transport / regulation of neuronal synaptic plasticity / monoatomic ion channel complex / positive regulation of excitatory postsynaptic potential / synaptic cleft / positive regulation of synaptic transmission, glutamatergic / calcium ion homeostasis / glutamate-gated receptor activity / presynaptic active zone membrane / glutamate-gated calcium ion channel activity / EPHB-mediated forward signaling / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / synaptic membrane / hippocampal mossy fiber to CA3 synapse / adult locomotory behavior / regulation of membrane potential / excitatory postsynaptic potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / brain development / postsynaptic density membrane / visual learning / regulation of synaptic plasticity / calcium ion transmembrane transport / long-term synaptic potentiation / terminal bouton / synaptic vesicle / signaling receptor activity / amyloid-beta binding / RAF/MAP kinase cascade / response to ethanol / chemical synaptic transmission / dendritic spine / postsynaptic membrane / calmodulin binding / neuron projection / postsynaptic density / dendrite / calcium ion binding / synapse / endoplasmic reticulum membrane / protein-containing complex binding / glutamatergic synapse / cell surface / positive regulation of transcription by RNA polymerase II / plasma membrane / cytoplasm
Similarity search - Function
: / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. ...: / : / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / 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 2D / Glutamate receptor ionotropic, NMDA 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsZhang JL / Zhu SJ / Guo F
Funding support China, 9 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31771115 China
National Natural Science Foundation of China (NSFC)31671049 China
National Natural Science Foundation of China (NSFC)81030065 China
Chinese Academy of SciencesXDB32020000 China
Chinese Academy of SciencesXDA12040214 China
Chinese Academy of SciencesXDA12040220 China
National Natural Science Foundation of China (NSFC)81803828 China
Chinese Academy of Sciences2019280 China
National Natural Science Foundation of China (NSFC)32221003 China
CitationJournal: To Be Published
Title: A novel antidepressant acting via allosteric inhibition of GluN2D-incorporated NMDA receptors at GABAergic interneurons
Authors: Zhang JL / Zhu SJ / Fei G
History
DepositionJan 25, 2024-
Header (metadata) releaseJan 22, 2025-
Map releaseJan 22, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38847.png

Downloads & links

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Map

FileDownload / File: emd_38847.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 280 pix.
= 299.88 Å		1.07 Å/pix.
x 280 pix.
= 299.88 Å		1.07 Å/pix.
x 280 pix.
= 299.88 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.071 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0123
Minimum - Maximum-0.019075792 - 0.04576813
Average (Standard dev.)0.00018440395 (±0.002284942)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 299.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_38847_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38847_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38847_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : N-methyl-D-aspartate receptors

EntireName: N-methyl-D-aspartate receptors
Components
  • Complex: N-methyl-D-aspartate receptors
    • Protein or peptide: Isoform 6 of Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2D
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(2~{S})-2-methyl-4-[(1~{R},2~{R},4~{S},6~{S},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S},18~{R})-7,9,13,18-tetramethyl-16-oxidanyl-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-yl]butoxy]oxane-3,4,5-triol

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Supramolecule #1: N-methyl-D-aspartate receptors

SupramoleculeName: N-methyl-D-aspartate receptors / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 400 kDa/nm

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Macromolecule #1: Isoform 6 of Glutamate receptor ionotropic, NMDA 1

MacromoleculeName: Isoform 6 of Glutamate receptor ionotropic, NMDA 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 97.777914 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSTMRLLTLA LLFSCSVARA ACDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYS W NHIILLVS ...String:
MSTMRLLTLA LLFSCSVARA ACDPKIVNIG AVLSTRKHEQ MFREAVNQAN KRHGSWKIQL NATSVTHKPN AIQMALSVCE DLISSQVYA ILVSHPPTPN DHFTPTPVSY TAGFYRIPVL GLTTRMSIYS DKSIHLSFLR TVPPYSHQSS VWFEMMRVYS W NHIILLVS DDHEGRAAQK RLETLLEERE SKSKKRNYEN LDQLSYDNKR GPKAEKVLQF DPGTKNVTAL LMEAKELEAR VI ILSASED DAATVYRAAA MLNMTGSGYV WLVGEREISG NALRYAPDGI LGLQLINGKN ESAHISDAVG VVAQAVHELL EKE NITDPP RGCVGNTNIW KTGPLFKRVL MSSKYADGVT GRVEFNEDGD RKFANYSIMN LQNRKLVQVG IYNGTHVIPN DRKI IWPGG ETEKPRGYQM STRLKIVTIH QEPFVYVKPT LSDGTCKEEF TVNGDPVKKV ICTGPNDTSP GSPRHTVPQC CYGFC IDLL IKLARTMNFT YEVHLVADGK FGTQERVNNS NKKEWNGMMG ELLSGQADMI VAPLTINNER AQYIEFSKPF KYQGLT ILV KKEIPRSTLD SFMQPFQSTL WLLVGLSVHV VAVMLYLLDR FSPFGRFKVN SEEEEEDALT LSSAMWFSWG VLLNSGI GE GAPRSFSARI LGMVWAGFAM IIVASYTANL AAFLVLDRPE ERITGINDPR LRNPSDKFIY ATVKQSSVDI YFRRQVEL S TMYRHMEKHN YESAAEAIQA VRDNKLHAFI WDSAVLEFEA SQKCDLVTTG ELFFRSGFGI GMRKDSPWKQ NVSLSILKS HENGFMEDLD KTWVRYQECD SRSNAPATLT FENMAGVFML VAGGIVAGIF LIFIEIAYKR HKDARRKQ

UniProtKB: Glutamate receptor ionotropic, NMDA 1

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Macromolecule #2: Glutamate receptor ionotropic, NMDA 2D

MacromoleculeName: Glutamate receptor ionotropic, NMDA 2D / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 99.057328 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRGAGGPRGP RGPAKMLLLL ALACASPFPE EAPGPGGAGG PGGGLGGARP LNVALVFSGP AYAAEAARLG PAVAAAVRSP GLDVRPVAL VLNGSDPRSL VLQLCDLLSG LRVHGVVFED DSRAPAVAPI LDFLSAQTSL PIVAVHGGAA LVLTPKEKGS T FLQLGSST ...String:
MRGAGGPRGP RGPAKMLLLL ALACASPFPE EAPGPGGAGG PGGGLGGARP LNVALVFSGP AYAAEAARLG PAVAAAVRSP GLDVRPVAL VLNGSDPRSL VLQLCDLLSG LRVHGVVFED DSRAPAVAPI LDFLSAQTSL PIVAVHGGAA LVLTPKEKGS T FLQLGSST EQQLQVIFEV LEEYDWTSFV AVTTRAPGHR AFLSYIEVLT DGSLVGWEHR GALTLDPGAG EAVLSAQLRS VS AQIRLLF CAREEAEPVF RAAEEAGLTG SGYVWFMVGP QLAGGGGSGA PGEPPLLPGG APLPAGLFAV RSAGWRDDLA RRV AAGVAV VARGAQALLR DYGFLPELGH DCRAQNRTHR GESLHRYFMN ITWDNRDYSF NEDGFLVNPS LVVISLTRDR TWEV VGSWE QQTLRLKYPL WSRYGRFLQP VDDTQHLTVA TLEERPFVIV EPADPISGTC IRDSVPCRSQ LNRTHSPPPD APRPE KRCC KGFCIDILKR LAHTIGFSYD LYLVTNGKHG KKIDGVWNGM IGEVFYQRAD MAIGSLTINE ERSEIVDFSV PFVETG ISV MVARSNGTVS PSAFLEPYSP AVWVMMFVMC LTVVAVTVFI FEYLSPVGYN RSLATGKRPG GSTFTIGKSI WLLWALV FN NSVPVENPRG TTSKIMVLVW AFFAVIFLAS YTANLAAFMI QEEYVDTVSG LSDRKFQRPQ EQYPPLKFGT VPNGSTEK N IRSNYPDMHS YMVRYNQPRV EEALTQLKAG KLDAFIYDAA VLNYMARKDE GCKLVTIGSG KVFATTGYGI ALHKGSRWK RPIDLALLQF LGDDEIEMLE RLWLSGICHN DKIEVMSSKL DIDNMAGVFY MLLVAMGLSL LVFAWEHLVY WRLRHCLGPA ASAWSHPQF EKGGGSGGGS GGSAWSHPQF EK

UniProtKB: Glutamate receptor ionotropic, NMDA 2D

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #4: (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(2~{S})-2-me...

MacromoleculeName: (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(2~{S})-2-methyl-4-[(1~{R},2~{R},4~{S},6~{S},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S},18~{R})-7,9,13,18-tetramethyl-16-oxidanyl-5- ...Name: (2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(2~{S})-2-methyl-4-[(1~{R},2~{R},4~{S},6~{S},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S},18~{R})-7,9,13,18-tetramethyl-16-oxidanyl-5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icosan-6-yl]butoxy]oxane-3,4,5-triol
type: ligand / ID: 4 / Number of copies: 2 / Formula: A1LW8
Molecular weightTheoretical: 592.804 Da

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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

Concentration2.0 mg/mL
BufferpH: 8
Sugar embeddingMaterial: nanodisc
Details: The protein sample of N-methyl-D-aspartate receptors was reconstructed into artificial nanodiscs composed by soya bean lecithin and MSP1E3D1 protein.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 46.4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-10 (5k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 6016 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 605501
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7yff

Final reconstructionNumber classes used: 3 / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 82019
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.1.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 22783 / Software - Name: RELION (ver. 3.1.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7yff


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8y1v:
Structure of GluN1b-GluN2D NMDA receptor in complex with competitive antagonist R-CPP and allosteric inhibitor YY-23

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