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- EMDB-27957: Glycine and glutamate bound Human GluN1a-GluN2D NMDA receptor -

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Basic information

Entry
Database: EMDB / ID: EMD-27957
TitleGlycine and glutamate bound Human GluN1a-GluN2D NMDA receptor
Map dataComposite map
Sample
  • Complex: Hetero-tetrameric GluN1a-GluN2D NMDA receptors
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2D
  • Ligand: GLYCINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GLUTAMIC ACID
KeywordsLigand-gated ion channel / ionotropic glutamate receptor / synaptic protein / voltage-gate ion channel / TRANSPORT PROTEIN
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: 3.38 Å
AuthorsKang H / Furukawa H
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS111745 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH085926 United States
CitationJournal: Mol Cell / Year: 2022
Title: Structural insights into assembly and function of GluN1-2C, GluN1-2A-2C, and GluN1-2D NMDARs.
Authors: Tsung-Han Chou / Hyunook Kang / Noriko Simorowski / Stephen F Traynelis / Hiro Furukawa /
Abstract: Neurotransmission mediated by diverse subtypes of N-methyl-D-aspartate receptors (NMDARs) is fundamental for basic brain functions and development as well as neuropsychiatric diseases and disorders. ...Neurotransmission mediated by diverse subtypes of N-methyl-D-aspartate receptors (NMDARs) is fundamental for basic brain functions and development as well as neuropsychiatric diseases and disorders. NMDARs are glycine- and glutamate-gated ion channels that exist as heterotetramers composed of obligatory GluN1 and GluN2(A-D) and/or GluN3(A-B). The GluN2C and GluN2D subunits form ion channels with distinct properties and spatio-temporal expression patterns. Here, we provide the structures of the agonist-bound human GluN1-2C NMDAR in the presence and absence of the GluN2C-selective positive allosteric potentiator (PAM), PYD-106, the agonist-bound GluN1-2A-2C tri-heteromeric NMDAR, and agonist-bound GluN1-2D NMDARs by single-particle electron cryomicroscopy. Our analysis shows unique inter-subunit and domain arrangements of the GluN2C NMDARs, which contribute to functional regulation and formation of the PAM binding pocket and is distinct from GluN2D NMDARs. Our findings here provide the fundamental blueprint to study GluN2C- and GluN2D-containing NMDARs, which are uniquely involved in neuropsychiatric disorders.
History
DepositionAug 26, 2022-
Header (metadata) releaseDec 7, 2022-
Map releaseDec 7, 2022-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27957.png

Downloads & links

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Map

FileDownload / File: emd_27957.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map
Projections & slices

Image control

Size
Brightness
Contrast
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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)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.05256967 - 1.2579536
Average (Standard dev.)0.006316933 (±0.020558001)
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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Additional map: ECD Local

Fileemd_27957_additional_1.map
AnnotationECD_Local
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: LBD Local

Fileemd_27957_additional_2.map
AnnotationLBD_Local
Projections & Slices
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Histogram

Histogram (log scale)

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Additional map: TMD Local

Fileemd_27957_additional_3.map
AnnotationTMD_Local
Projections & Slices
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Sample components

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Entire : Hetero-tetrameric GluN1a-GluN2D NMDA receptors

EntireName: Hetero-tetrameric GluN1a-GluN2D NMDA receptors
Components
  • Complex: Hetero-tetrameric GluN1a-GluN2D NMDA receptors
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 2D
  • Ligand: GLYCINE
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GLUTAMIC ACID

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Supramolecule #1: Hetero-tetrameric GluN1a-GluN2D NMDA receptors

SupramoleculeName: Hetero-tetrameric GluN1a-GluN2D NMDA receptors / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 93.07825 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: RAASDPKIVN IGAVLSTRKH EQMFREAVNQ ANKRHGSWKI QLNATSVTHK PNAIQMALSV CEDLISSQVY AILVSHPPTP NDHFTPTPV SYTAGFYRIP VLGLTTRMSI YSDKSIHLSF LRTVPPYSHQ SSVWFEMMRV YSWNHIILLV SDDHEGRAAQ K RLETLLEE ...String:
RAASDPKIVN IGAVLSTRKH EQMFREAVNQ ANKRHGSWKI QLNATSVTHK PNAIQMALSV CEDLISSQVY AILVSHPPTP NDHFTPTPV SYTAGFYRIP VLGLTTRMSI YSDKSIHLSF LRTVPPYSHQ SSVWFEMMRV YSWNHIILLV SDDHEGRAAQ K RLETLLEE RESKAEKVLQ FDPGTKNVTA LLMEAKELEA RVIILSASED DAATVYRAAA MLNMTGSGYV WLVGEREISG NA LRYAPDG ILGLQLINGK NESAHISDAV GVVAQAVHEL LEKENITDPP RGCVGNTNIW KTGPLFKRVL MSSKYADGVT GRV EFNEDG DRKFANYSIM NLQNRKLVQV GIYNGTHVIP NDRKIIWPGG ETEKPRGYQM STRLKIVTIH QEPFVYVKPT LSDG TCKEE FTVNGDPVKK VICTGPNDTS PGSPRHTVPQ CCYGFCIDLL IKLARTMNFT YEVHLVADGK FGTQERVNNS NKKEW NGMM GELLSGQADM IVAPLTINNE RAQYIEFSKP FKYQGLTILV KKEIPRSTLD SFMQPFQSTL WLLVGLSVHV VAVMLY LLD RFSPFGRFKV NSEEEEEDAL TLSSAMWFSW GVLLNSGIGE GAPRSFSARI LGMVWAGFAM IIVASYTANL AAFLVLD RP EERITGINDP RLRNPSDKFI YATVKQSSVD IYFRRQVELS TMYRHMEKHN YESAAEAIQA VRDNKLHAFI WDSAVLEF E ASQKCDLVTT GELFFRSGFG IGMRKDSPWK QNVSLSILKS HENGFMEDLD KTWVRYQECD SRSNAPATLT FENMAGVFM LVAGGIVAGI FLIFIEIAYK RHKDANGAQ

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: 96.760492 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: WSHPQFEKGG GSGGGSGGSA WSHPQFEKGA LVPRGFPEEA PGPGGAGGPG GGLGGARPLN VALVFSGPAY AAEAARLGPA VAAAVRSPG LDVRPVALVL NGSDPRSLVL QLCDLLSGLR VHGVVFEDDS RAPAVAPILD FLSAQTSLPI VAVHGGAALV L TPKEKGST ...String:
WSHPQFEKGG GSGGGSGGSA WSHPQFEKGA LVPRGFPEEA PGPGGAGGPG GGLGGARPLN VALVFSGPAY AAEAARLGPA VAAAVRSPG LDVRPVALVL NGSDPRSLVL QLCDLLSGLR VHGVVFEDDS RAPAVAPILD FLSAQTSLPI VAVHGGAALV L TPKEKGST FLQLGSSTEQ QLQVIFEVLE EYDWTSFVAV TTRAPGHRAF LSYIEVLTDG SLVGWEHRGA LTLDPGAGEA VL SAQLRSV SAQIRLLFCA REEAEPVFRA AEEAGLTGSG YVWFMVGPQL AGGGGSGAPG EPPLLPGGAP LPAGLFAVRS AGW RDDLAR RVAAGVAVVA RGAQALLRDY GFLPELGHDC RAQNRTHRGE SLHRYFMNIT WDNRDYSFNE DGFLVNPSLV VISL TRDRT WEVVGSWEQQ TLRLKYPLWS RYGRFLQPVD DTQHLTVATL EERPFVIVEP ADPISGTCIR DSVPCRSQLN RTHSP PPDA PRPEKRCCKG FCIDILKRLA HTIGFSYDLY LVTNGKHGKK IDGVWNGMIG EVFYQRADMA IGSLTINEER SEIVDF SVP FVETGISVMV ARSNGTVSPS AFLEPYSPAV WVMMFVMCLT VVAVTVFIFE YLSPVGYNRS LATGKRPGGS TFTIGKS IW LLWALVFNNS VPVENPRGTT SKIMVLVWAF FAVIFLASYT ANLAAFMIQE EYVDTVSGLS DRKFQRPQEQ YPPLKFGT V PNGSTEKNIR SNYPDMHSYM VRYNQPRVEE ALTQLKAGKL DAFIYDAAVL NYMARKDEGC KLVTIGSGKV FATTGYGIA LHKGSRWKRP IDLALLQFLG DDEIEMLERL WLSGICHNDK IEVMSSKLDI DNMAGVFYML LVAMGLSLLV FAWEHLVYWR LRHCLGP

UniProtKB: Glutamate receptor ionotropic, NMDA 2D

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Macromolecule #3: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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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: GLUTAMIC ACID

MacromoleculeName: GLUTAMIC ACID / type: ligand / ID: 5 / Number of copies: 2 / Formula: GLU
Molecular weightTheoretical: 147.129 Da
Chemical component information

ChemComp-GLU:
GLUTAMIC 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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 74.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 8012932
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7saa

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 199693
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)

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Atomic model buiding 1

Initial model
PDB IDChain

3oel

chain_id: A, source_name: PDB, initial_model_type: experimental model

7saa

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-8e96:
Glycine and glutamate bound Human GluN1a-GluN2D NMDA receptor

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