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Yorodumi- PDB-6irf: Structure of the human GluN1/GluN2A NMDA receptor in the glutamat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6irf | ||||||||||||||||||
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Title | Structure of the human GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at pH 6.3, Class I | ||||||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / ionotropic glutamate receptors / NMDA receptors / synaptic protein | ||||||||||||||||||
Function / homology | Function and homology information excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / sleep / activation of cysteine-type endopeptidase activity / glutamate-gated calcium ion channel activity ...excitatory chemical synaptic transmission / directional locomotion / Synaptic adhesion-like molecules / serotonin metabolic process / protein localization to postsynaptic membrane / propylene metabolic process / response to glycine / sleep / activation of cysteine-type endopeptidase activity / glutamate-gated calcium ion channel activity / Assembly and cell surface presentation of NMDA receptors / glutamate receptor signaling pathway / regulation of monoatomic cation transmembrane transport / Neurexins and neuroligins / NMDA glutamate receptor activity / NMDA selective glutamate receptor complex / calcium ion transmembrane import into cytosol / protein heterotetramerization / glutamate binding / positive regulation of reactive oxygen species biosynthetic process / startle response / glycine binding / positive regulation of calcium ion transport into cytosol / regulation of neuronal synaptic plasticity / dopamine metabolic process / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / monoatomic cation transmembrane transport / ligand-gated monoatomic ion channel activity / monoatomic cation transport / positive regulation of excitatory postsynaptic potential / Long-term potentiation / excitatory synapse / calcium ion homeostasis / synaptic cleft / response to amphetamine / MECP2 regulates neuronal receptors and channels / sensory perception of pain / EPHB-mediated forward signaling / excitatory postsynaptic potential / regulation of membrane potential / ionotropic glutamate receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / neurogenesis / positive regulation of synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / long-term synaptic potentiation / postsynaptic density membrane / visual learning / brain development / protein catabolic process / regulation of synaptic plasticity / memory / cytoplasmic vesicle membrane / negative regulation of protein catabolic process / terminal bouton / response to wounding / synaptic vesicle / presynaptic membrane / signaling receptor activity / amyloid-beta binding / chemical synaptic transmission / postsynaptic membrane / RAF/MAP kinase cascade / response to ethanol / dendritic spine / postsynaptic density / learning or memory / calmodulin binding / neuron projection / response to xenobiotic stimulus / positive regulation of apoptotic process / dendrite / glutamatergic synapse / synapse / calcium ion binding / protein-containing complex binding / endoplasmic reticulum membrane / cell surface / positive regulation of transcription by RNA polymerase II / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 Å | ||||||||||||||||||
Authors | Zhang, J. / Chang, S. / Zhang, X. / Zhu, S. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Cell Rep / Year: 2018 Title: Structural Basis of the Proton Sensitivity of Human GluN1-GluN2A NMDA Receptors. Authors: Jin-Bao Zhang / Shenghai Chang / Pan Xu / Miao Miao / Hangjun Wu / Youyi Zhang / Tongtong Zhang / Han Wang / Jilin Zhang / Chun Xie / Nan Song / Cheng Luo / Xing Zhang / Shujia Zhu / Abstract: N-methyl-D-aspartate (NMDA) receptors are critical for synaptic development and plasticity. While glutamate is the primary agonist, protons can modulate NMDA receptor activity at synapses during ...N-methyl-D-aspartate (NMDA) receptors are critical for synaptic development and plasticity. While glutamate is the primary agonist, protons can modulate NMDA receptor activity at synapses during vesicle exocytosis by mechanisms that are unknown. We used cryo-electron microscopy to solve the structures of the human GluN1-GluN2A NMDA receptor at pH 7.8 and pH 6.3. Our structures demonstrate that the proton sensor predominantly resides in the N-terminal domain (NTD) of the GluN2A subunit and reveal the allosteric coupling mechanism between the proton sensor and the channel gate. Under high-pH conditions, the GluN2A-NTD adopts an "open-and-twisted" conformation. However, upon protonation at the lower pH, the GluN2A-NTD transits from an open- to closed-cleft conformation, causing rearrangements between the tetrameric NTDs and agonist-binding domains. The conformational mobility observed in our structures (presumably from protonation) is supported by molecular dynamics simulation. Our findings reveal the structural mechanisms by which protons allosterically inhibit human GluN1-GluN2A receptor activity. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6irf.cif.gz | 530.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6irf.ent.gz | 443 KB | Display | PDB format |
PDBx/mmJSON format | 6irf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ir/6irf ftp://data.pdbj.org/pub/pdb/validation_reports/ir/6irf | HTTPS FTP |
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-Related structure data
Related structure data | 9715MC 9714C 9716C 9717C 6iraC 6irgC 6irhC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 95336.219 Da / Num. of mol.: 2 / Mutation: G612R Source method: isolated from a genetically manipulated source Details: 2 mM Glycine / Source: (gene. exp.) Homo sapiens (human) / Gene: Grin1, NMDAR1 / Cell line (production host): HEK293S GnTl- / Production host: Homo sapiens (human) / References: UniProt: Q05586 #2: Protein | Mass: 94192.172 Da / Num. of mol.: 2 / Mutation: E656R, E657R Source method: isolated from a genetically manipulated source Details: 2 mM L-Glutamate / Source: (gene. exp.) Homo sapiens (human) / Gene: Grin2a / Cell line (production host): HEK293S GnTl- / Production host: Homo sapiens (human) / References: UniProt: Q12879 |
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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: Human GluN1/GluN2A NMDA receptors in the glutamate/glycine bound state at pH 6.3, Class I Type: COMPLEX / Details: with the presence of Glycine,L-glutamate and EDTA / Entity ID: all / Source: RECOMBINANT | |||||||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 0.38 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: Homo sapiens (human) | |||||||||||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293S GnTl- / Plasmid: pEG-Bacmam | |||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 6.3 / Details: Solutions were made fresh. | |||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Tetrameric GluN1/GluN2A NMDA receptors | |||||||||||||||||||||||||||||||||||||||||||||
Specimen support | Details: 15 mA / Grid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K Details: blot for 2 seconds before plunging in liquid 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 FIELDBright-field microscopy |
Image recording | Average exposure time: 12 sec. / Electron dose: 56 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4 |
Image scans | Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 722287 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 193878 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||
Atomic model building |
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