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- PDB-8usw: CNQX-bound GluN1a-3A NMDA receptor -

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Basic information

Entry
Database: PDB / ID: 8usw
TitleCNQX-bound GluN1a-3A NMDA receptor
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 3A
KeywordsMEMBRANE PROTEIN / Channel / receptor
Function / homology
Function and homology information


serine binding / negative regulation of dendritic spine development / glycine-gated cation channel activity / pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion ...serine binding / negative regulation of dendritic spine development / glycine-gated cation channel activity / pons maturation / positive regulation of Schwann cell migration / regulation of cell communication / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / olfactory learning / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / transmitter-gated monoatomic ion channel activity / suckling behavior / 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 / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / voltage-gated monoatomic cation channel activity / response to glycoside / NMDA selective glutamate receptor complex / neurotransmitter receptor complex / ligand-gated sodium channel activity / glutamate binding / response to morphine / calcium ion transmembrane import into cytosol / regulation of axonogenesis / neuromuscular process / regulation of dendrite morphogenesis / protein heterotetramerization / male mating behavior / glycine binding / regulation of synapse assembly / response to amine / parallel fiber to Purkinje cell synapse / startle response / positive regulation of reactive oxygen species biosynthetic process / monoatomic cation transmembrane transport / dendrite development / positive regulation of calcium ion transport into cytosol / regulation of neuron apoptotic process / associative learning / cellular response to glycine / monoatomic cation transport / excitatory synapse / positive regulation of dendritic spine maintenance / social behavior / regulation of neuronal synaptic plasticity / monoatomic ion channel complex / positive regulation of excitatory postsynaptic potential / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / long-term memory / positive regulation of synaptic transmission, glutamatergic / synaptic cleft / prepulse inhibition / phosphatase binding / monoatomic cation channel activity / calcium ion homeostasis / response to fungicide / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / cellular response to manganese ion / presynaptic active zone membrane / sensory perception of pain / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / presynaptic modulation of chemical synaptic transmission / sodium ion transmembrane transport / ionotropic glutamate receptor signaling pathway / synaptic membrane / protein phosphatase 2A binding / hippocampal mossy fiber to CA3 synapse / response to amphetamine / adult locomotory behavior / excitatory postsynaptic potential / regulation of membrane potential / learning / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / regulation of long-term neuronal synaptic plasticity / response to calcium ion / postsynaptic density membrane / modulation of chemical synaptic transmission / neuron cellular homeostasis / calcium ion transmembrane transport / visual learning / regulation of synaptic plasticity / cerebral cortex development / calcium channel activity / memory / intracellular calcium ion homeostasis / terminal bouton / synaptic vesicle / synaptic vesicle membrane
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.23 Å
AuthorsMichalski, K. / Furukawa, H.
Funding support United States, 4items
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
DepositionOct 30, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 3A
C: Glutamate receptor ionotropic, NMDA 1
D: Glutamate receptor ionotropic, NMDA 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)400,2226
Polymers399,7584
Non-polymers4642
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Glutamate receptor ionotropic, NMDA 1


Mass: 95041.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Grin1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P35439
#2: Protein Glutamate receptor ionotropic, NMDA 3A


Mass: 104837.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN3A / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TCU5
#3: Chemical ChemComp-DQC / 7-nitro-2,3-dioxo-1,2,3,4-tetrahydroquinoxaline-6-carbonitrile


Mass: 232.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H4N4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CNQX-bound GluN1-3A NMDA receptor / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.4 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: cryoSPARC / Category: 3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 4.23 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 264487 / Symmetry type: POINT

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