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- EMDB-42580: Glycine-bound GluN1a-3A LBD heterotetramer (local refinement) -

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Basic information

Entry
Database: EMDB / ID: EMD-42580
TitleGlycine-bound GluN1a-3A LBD heterotetramer (local refinement)
Map data
Sample
  • Complex: Glycine-bound GluN1-3A LBD heterotetramer (local refinement)
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 3A
KeywordsChannel / receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


serine binding / negative regulation of dendritic spine development / neurotransmitter receptor complex / excitatory chemical synaptic transmission / Synaptic adhesion-like molecules / response to glycine / propylene metabolic process / glutamate receptor activity / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors ...serine binding / negative regulation of dendritic spine development / neurotransmitter receptor complex / excitatory chemical synaptic transmission / Synaptic adhesion-like molecules / response to glycine / propylene metabolic process / glutamate receptor activity / regulation of monoatomic cation transmembrane transport / Assembly and cell surface presentation of NMDA receptors / NMDA glutamate receptor activity / Neurexins and neuroligins / transmitter-gated monoatomic ion channel activity / NMDA selective glutamate receptor complex / ligand-gated sodium channel activity / calcium ion transmembrane import into cytosol / glutamate binding / protein heterotetramerization / glycine binding / positive regulation of reactive oxygen species biosynthetic process / positive regulation of calcium ion transport into cytosol / Negative regulation of NMDA receptor-mediated neuronal transmission / monoatomic ion channel complex / Unblocking of NMDA receptors, glutamate binding and activation / dendrite development / monoatomic cation transmembrane transport / regulation of neuronal synaptic plasticity / monoatomic cation transport / Long-term potentiation / positive regulation of excitatory postsynaptic potential / excitatory synapse / ligand-gated monoatomic ion channel activity / synaptic cleft / prepulse inhibition / calcium ion homeostasis / glutamate-gated calcium ion channel activity / EPHB-mediated forward signaling / presynaptic modulation of chemical synaptic transmission / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / positive regulation of synaptic transmission, glutamatergic / protein phosphatase 2A binding / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / excitatory postsynaptic potential / synaptic transmission, glutamatergic / synaptic membrane / modulation of chemical synaptic transmission / postsynaptic density membrane / visual learning / terminal bouton / brain development / regulation of synaptic plasticity / calcium channel activity / calcium ion transmembrane transport / calcium ion transport / rhythmic process / synaptic vesicle / signaling receptor activity / presynapse / amyloid-beta binding / RAF/MAP kinase cascade / chemical synaptic transmission / response to ethanol / postsynaptic membrane / dendritic spine / calmodulin binding / postsynaptic density / neuron projection / neuronal cell body / dendrite / calcium ion binding / synapse / endoplasmic reticulum membrane / protein-containing complex binding / glutamatergic synapse / cell surface / positive regulation of transcription by RNA polymerase II / identical protein binding / membrane / 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 1 / Glutamate receptor ionotropic, NMDA 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsMichalski K / Furukawa H
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)NS11745 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)MH085926 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)F32MH121061 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)NS113632 United States
CitationJournal: Sci Adv / Year: 2024
Title: Structure and function of GluN1-3A NMDA receptor excitatory glycine receptor channel.
Authors: Kevin Michalski / Hiro Furukawa /
Abstract: -methyl-d-aspartate receptors (NMDARs) and other ionotropic glutamate receptors (iGluRs) mediate most of the excitatory signaling in the mammalian brains in response to the neurotransmitter glutamate. ...-methyl-d-aspartate receptors (NMDARs) and other ionotropic glutamate receptors (iGluRs) mediate most of the excitatory signaling in the mammalian brains in response to the neurotransmitter glutamate. Uniquely, NMDARs composed of GluN1 and GluN3 are activated exclusively by glycine, the neurotransmitter conventionally mediating inhibitory signaling when it binds to pentameric glycine receptors. The GluN1-3 NMDARs are vital for regulating neuronal excitability, circuit function, and specific behaviors, yet our understanding of their functional mechanism at the molecular level has remained limited. Here, we present cryo-electron microscopy structures of GluN1-3A NMDARs bound to an antagonist, CNQX, and an agonist, glycine. The structures show a 1-3-1-3 subunit heterotetrameric arrangement and an unprecedented pattern of GluN3A subunit orientation shift between the glycine-bound and CNQX-bound structures. Site-directed disruption of the unique subunit interface in the glycine-bound structure mitigated desensitization. Our study provides a foundation for understanding the distinct structural dynamics of GluN3 that are linked to the unique function of GluN1-3 NMDARs.
History
DepositionNov 1, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42580.png

Downloads & links

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Map

FileDownload / File: emd_42580.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.856 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.266
Minimum - Maximum-1.5074983 - 2.4032974
Average (Standard dev.)-0.000003894947 (±0.038950413)
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: #1

Fileemd_42580_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42580_half_map_2.map
Projections & Slices
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Sample components

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Entire : Glycine-bound GluN1-3A LBD heterotetramer (local refinement)

EntireName: Glycine-bound GluN1-3A LBD heterotetramer (local refinement)
Components
  • Complex: Glycine-bound GluN1-3A LBD heterotetramer (local refinement)
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 1
    • Protein or peptide: Glutamate receptor ionotropic, NMDA 3A

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Supramolecule #1: Glycine-bound GluN1-3A LBD heterotetramer (local refinement)

SupramoleculeName: Glycine-bound GluN1-3A LBD heterotetramer (local refinement)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 400 KDa

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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: 45.902477 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: STRLKIVTIH QEPFVYVKPT MSDGTCKEEF TVNGDPVKKV ICTGPNDTSP GSPRHTVPQC CYGFCIDLLI KLARTMNFTY EVHLVADGK FGTQERVNNS NKKEWNGMMG ELLSGQADMI VAPLTINNER AQYIEFSKPF KYQGLTILVK KEIPRSTLDS F MQPFQSTL ...String:
STRLKIVTIH QEPFVYVKPT MSDGTCKEEF TVNGDPVKKV ICTGPNDTSP GSPRHTVPQC CYGFCIDLLI KLARTMNFTY EVHLVADGK FGTQERVNNS NKKEWNGMMG ELLSGQADMI VAPLTINNER AQYIEFSKPF KYQGLTILVK KEIPRSTLDS F MQPFQSTL WLLVGLSVHV VAVMLYLLDR FSPFGRFKVN SEEEEEDALT LSSAMWFSWG VLLNSGIGEG APRSFSARIL GM VWAGFAM IIVASYTANL AAFLVLDRPE ERITGINDPR LRNPSDKFIY ATVKQSSVDI YFRRQVELST MYRHMEKHNY ESA AEAIQA VRDNKLHAFI WDSAVLEFEA SQKCDLVTTG ELFFRSGFGI GMRKDSPWKQ NVSLSILKSH ENGFMEDLDK TWVR YQEC

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: Homo sapiens (human)
Molecular weightTheoretical: 45.53532 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: SKLHLRVVTL IEHPFVFTRE VDDEGLCPAG QLCLDPMTND SSTLDSLFSS LHSSNDTVPI KFKKCCYGYC IDLLEKIAED MNFDFDLYI VGDGKYGAWK NGHWTGLVGD LLRGTAHMAV TSFSINTARS QVIDFTSPFF STSLGILVRT RDTAAPIGAF M WPLHWTMW ...String:
SKLHLRVVTL IEHPFVFTRE VDDEGLCPAG QLCLDPMTND SSTLDSLFSS LHSSNDTVPI KFKKCCYGYC IDLLEKIAED MNFDFDLYI VGDGKYGAWK NGHWTGLVGD LLRGTAHMAV TSFSINTARS QVIDFTSPFF STSLGILVRT RDTAAPIGAF M WPLHWTMW LGIFVALHIT AVFLTLYEWK SPFGLTPKGR NRSKVFSFSS ALNICYALLF GRTVAIKPPK CWTGRFLMNL WA IFCMFCL STYTANLAAV MVGEKIYEEL SGIHDPKLHH PSQGFRFGTV RESSAEDYVR QSFPEMHEYM RRYNVPATPD GVE YLKNDP EKLDAFIMDK ALLDYEVSID ADCKLLTVGK PFAIEGYGIG LPPNSPLTAN ISELISQYKS HGFMDMLHDK WYRV VPC

UniProtKB: Glutamate receptor ionotropic, NMDA 3A

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / 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

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 225900
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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