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Yorodumi- PDB-8jf7: Triheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jf7 | ||||||
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Title | Triheteromeric NMDA receptor GluN1-GluN2A-GluN3A in complex with glycine, glutamate, a GluN1-specific Fab,and a GluN2A-specific Fab | ||||||
Components |
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Keywords | MEMBRANE 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 / pons maturation / regulation of cell communication / positive regulation of Schwann cell migration / response to environmental enrichment ...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 / 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 place preference / 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 / voltage-gated monoatomic cation channel activity / sleep / cellular response to dsRNA / dendritic spine organization / response to carbohydrate / regulation of monoatomic cation transmembrane transport / cellular response to lipid / glutamate receptor activity / locomotion / response to morphine / NMDA glutamate receptor activity / Synaptic adhesion-like molecules / regulation of NMDA receptor activity / NMDA selective glutamate receptor complex / RAF/MAP kinase cascade / glutamate-gated calcium ion channel activity / parallel fiber to Purkinje cell synapse / response to manganese ion / calcium ion transmembrane import into cytosol / protein heterotetramerization / glutamate binding / neuromuscular process / cellular response to zinc ion / positive regulation of reactive oxygen species biosynthetic process / regulation of synapse assembly / action potential / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of dendrite morphogenesis / regulation of axonogenesis / male mating behavior / spinal cord development / dopamine metabolic process / suckling behavior / startle response / dendrite development / response to amine / monoatomic cation transmembrane transport / monoatomic cation transport / regulation of neuronal synaptic plasticity / modulation of excitatory postsynaptic potential / response to lithium ion / associative learning / positive regulation of excitatory postsynaptic potential / social behavior / ligand-gated monoatomic ion channel activity / cellular response to glycine / excitatory synapse / positive regulation of dendritic spine maintenance / response to light stimulus / neuron development / positive regulation of protein targeting to membrane / Unblocking of NMDA receptors, glutamate binding and activation / phosphatase binding / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / cellular response to manganese ion / calcium ion homeostasis / glutamate receptor binding / prepulse inhibition / multicellular organismal response to stress / monoatomic cation channel activity / long-term memory / regulation of neuron apoptotic process / synaptic cleft / glutamate-gated receptor activity / presynaptic active zone membrane / 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 | ||||||
Biological species | Rattus norvegicus (Norway rat) Muromegalovirus G4 Mus musculus (house mouse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.73 Å | ||||||
Authors | Kou, Z. / Zhu, S. | ||||||
Funding support | China, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jf7.cif.gz | 713.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jf7.ent.gz | 571.6 KB | Display | PDB format |
PDBx/mmJSON format | 8jf7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jf7_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8jf7_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8jf7_validation.xml.gz | 116.9 KB | Display | |
Data in CIF | 8jf7_validation.cif.gz | 175.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jf/8jf7 ftp://data.pdbj.org/pub/pdb/validation_reports/jf/8jf7 | HTTPS FTP |
-Related structure data
Related structure data | 36209MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Glutamate receptor ionotropic, NMDA ... , 3 types, 4 molecules ACBD
#1: Protein | 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 | | 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 | | 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 | 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 | 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 | | 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 | | 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
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 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 |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 7.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 162395 / Symmetry type: POINT | ||||||||||||||||||||||||
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