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- PDB-8jf7: Triheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with ... -

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Basic information

Entry
Database: PDB / ID: 8jf7
TitleTriheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with glycine, glutamate, a GluN1-specific Fab,and a GluN2A-specific Fab
Components
  • (GluN1-specific antibody fragment ...) x 2
  • (GluN2A-specific antibody fragment ...) x 2
  • (Glutamate receptor ionotropic, NMDA ...) x 3
KeywordsMEMBRANE PROTEIN / ion channel
Function / homology
Function and homology information


neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / negative regulation of dendritic spine development / directional locomotion / conditioned place preference / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration ...neurotransmitter receptor transport, plasma membrane to endosome / regulation of response to alcohol / response to ammonium ion / receptor recycling / negative regulation of dendritic spine development / directional locomotion / conditioned place preference / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / response to environmental enrichment / EPHB-mediated forward signaling / Assembly and cell surface presentation of NMDA receptors / response to hydrogen sulfide / olfactory learning / serotonin metabolic process / conditioned taste aversion / dendritic branch / regulation of respiratory gaseous exchange / protein localization to postsynaptic membrane / response to other organism / positive regulation of inhibitory postsynaptic potential / propylene metabolic process / response to glycine / regulation of ARF protein signal transduction / cellular response to magnesium ion / response to methylmercury / sleep / voltage-gated monoatomic cation channel activity / cellular response to dsRNA / dendritic spine organization / response to carbohydrate / locomotion / regulation of monoatomic cation transmembrane transport / response to morphine / cellular response to lipid / glutamate receptor activity / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / NMDA selective glutamate receptor complex / glutamate-gated calcium ion channel activity / parallel fiber to Purkinje cell synapse / response to manganese ion / calcium ion transmembrane import into cytosol / regulation of NMDA receptor activity / protein heterotetramerization / glutamate binding / cellular response to zinc ion / positive regulation of reactive oxygen species biosynthetic process / neuromuscular process / regulation of synapse assembly / action potential / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of dendrite morphogenesis / male mating behavior / regulation of axonogenesis / spinal cord development / dopamine metabolic process / suckling behavior / startle response / monoatomic cation transmembrane transport / dendrite development / regulation of neuronal synaptic plasticity / response to amine / modulation of excitatory postsynaptic potential / response to lithium ion / social behavior / associative learning / positive regulation of excitatory postsynaptic potential / monoatomic cation transport / ligand-gated monoatomic ion channel activity / excitatory synapse / cellular response to glycine / positive regulation of dendritic spine maintenance / response to light stimulus / Unblocking of NMDA receptors, glutamate binding and activation / neuron development / positive regulation of protein targeting to membrane / regulation of postsynaptic membrane potential / phosphatase binding / glutamate receptor binding / postsynaptic density, intracellular component / calcium ion homeostasis / cellular response to manganese ion / prepulse inhibition / multicellular organismal response to stress / long-term memory / monoatomic cation channel activity / regulation of neuron apoptotic process / presynaptic active zone membrane / synaptic cleft / glutamate-gated receptor activity / response to fungicide / sensory perception of pain / cell adhesion molecule binding / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / response to amphetamine
Similarity search - Function
: / : / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Green fluorescent protein, GFP / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Green fluorescent protein-related ...: / : / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / N-methyl D-aspartate receptor 2B3 C-terminus / Green fluorescent protein, GFP / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Green fluorescent protein-related / Green fluorescent protein / : / Green fluorescent protein / 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
Enhanced green fluorescent protein / Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A / Glutamate receptor ionotropic, NMDA 3A
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Muromegalovirus G4
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.73 Å
AuthorsKou, Z. / Zhu, S.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Probing the architecture of native GluN1-N2-N3A NMDA receptors by cryo-EM and click chemistry.
Authors: Kou, Z. / Zhu, S.
History
DepositionMay 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 2A,Enhanced green fluorescent protein
C: Glutamate receptor ionotropic, NMDA 1
D: Glutamate receptor ionotropic, NMDA 3A,Enhanced green fluorescent protein
E: GluN1-specific antibody fragment light chain
F: GluN1-specific antibody fragment heavy chain
G: GluN1-specific antibody fragment light chain
H: GluN1-specific antibody fragment heavy chain
K: GluN2A-specific antibody fragment light chain
J: GluN2A-specific antibody fragment heavy chain


Theoretical massNumber of molelcules
Total (without water)599,94810
Polymers599,94810
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Glutamate receptor ionotropic, NMDA ... , 3 types, 4 molecules ACBD

#1: Protein Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 95372.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Grin1, Nmdar1 / Production host: Homo sapiens (human) / References: UniProt: P35439
#2: Protein Glutamate receptor ionotropic, NMDA 2A,Enhanced green fluorescent protein / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / ...GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / NMDAR2A / NR2A


Mass: 125325.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Muromegalovirus G4
Gene: Grin2a, eGFP / Production host: Homo sapiens (human) / References: UniProt: Q00959, UniProt: A0A7G8ZY66
#3: Protein Glutamate receptor ionotropic, NMDA 3A,Enhanced green fluorescent protein / GluN3A / Glutamate receptor chi-1 / N-methyl-D-aspartate receptor / N-methyl-D-aspartate receptor ...GluN3A / Glutamate receptor chi-1 / N-methyl-D-aspartate receptor / N-methyl-D-aspartate receptor subtype 3A / NMDAR3A / NR3A / NMDAR-L / NMDAR-L1


Mass: 137362.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Muromegalovirus G4
Gene: Grin3a, eGFP / Production host: Homo sapiens (human) / References: UniProt: Q9R1M7, UniProt: A0A7G8ZY66

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Antibody , 4 types, 6 molecules EGFHKJ

#4: Antibody GluN1-specific antibody fragment light chain


Mass: 25739.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#5: Antibody GluN1-specific antibody fragment heavy chain


Mass: 23432.072 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#6: Antibody GluN2A-specific antibody fragment light chain


Mass: 23234.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#7: Antibody GluN2A-specific antibody fragment heavy chain


Mass: 24936.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)

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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: Triheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with glycine, glutamate, a GluN1-specific Fab,and a GluN2A-specific Fab
Type: COMPLEX / Entity ID: #4-#5, #1-#3, #7, #6 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 162395 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00230527
ELECTRON MICROSCOPYf_angle_d0.38541503
ELECTRON MICROSCOPYf_dihedral_angle_d7.17218267
ELECTRON MICROSCOPYf_chiral_restr0.0374703
ELECTRON MICROSCOPYf_plane_restr0.0035389

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