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- PDB-6ira: Structure of the human GluN1/GluN2A NMDA receptor in the glutamat... -

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Entry
Database: PDB / ID: 6ira
TitleStructure of the human GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at pH 7.8
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2A
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptors / NMDA receptors / synaptic protein
Function / homologyReceptor, ligand binding region / RAF/MAP kinase cascade / Periplasmic binding protein-like I / Receptor family ligand binding region / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / N-methyl D-aspartate receptor 2B3 C-terminus / Ligated ion channel L-glutamate- and glycine-binding site / EPHB-mediated forward signaling ...Receptor, ligand binding region / RAF/MAP kinase cascade / Periplasmic binding protein-like I / Receptor family ligand binding region / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / N-methyl D-aspartate receptor 2B3 C-terminus / Ligated ion channel L-glutamate- and glycine-binding site / EPHB-mediated forward signaling / Ras activation upon Ca2+ influx through NMDA receptor / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / Unblocking of NMDA receptors, glutamate binding and activation / Neurexins and neuroligins / MECP2 regulates neuronal receptors and channels / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor / Long-term potentiation / Synaptic adhesion-like molecules / Negative regulation of NMDA receptor-mediated neuronal transmission / Ligand-gated ion channel / propylene metabolic process / pons maturation / response to glycine / protein localization to postsynaptic membrane / directional locomotion / excitatory chemical synaptic transmission / conditioned taste aversion / olfactory learning / regulation of respiratory gaseous exchange / serotonin metabolic process / glutamate receptor signaling pathway / startle response / regulation of synapse assembly / sleep / glutamate-gated calcium ion channel activity / neurotransmitter binding / calcium ion transmembrane import into cytosol / cation transport / neurogenesis / respiratory gaseous exchange / calcium ion homeostasis / activation of cysteine-type endopeptidase activity / glycine binding / NMDA glutamate receptor activity / glutamate binding / NMDA selective glutamate receptor complex / dopamine metabolic process / regulation of dendrite morphogenesis / suckling behavior / synaptic membrane / positive regulation of cysteine-type endopeptidase activity / social behavior / positive regulation of reactive oxygen species biosynthetic process / male mating behavior / regulation of axonogenesis / synaptic transmission, glutamatergic / postsynaptic density membrane / response to morphine / positive regulation of calcium ion transport into cytosol / excitatory synapse / long-term memory / excitatory postsynaptic potential / synaptic cleft / positive regulation of excitatory postsynaptic potential / prepulse inhibition / regulation of membrane potential / adult locomotory behavior / sensory perception of pain / integral component of postsynaptic density membrane / regulation of sensory perception of pain / response to amphetamine / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / visual learning / regulation of synaptic plasticity / long-term synaptic potentiation / ionotropic glutamate receptor signaling pathway / cerebral cortex development / regulation of long-term neuronal synaptic plasticity / memory / positive regulation of long-term synaptic potentiation / terminal bouton / presynaptic membrane / ephrin receptor signaling pathway / negative regulation of protein catabolic process / protein heterotetramerization / postsynaptic membrane / synaptic vesicle / response to wounding / learning or memory / brain development / Ras guanyl-nucleotide exchange factor activity / chemical synaptic transmission / amyloid-beta binding / calmodulin binding / response to ethanol / negative regulation of neuron apoptotic process / dendritic spine / MAPK cascade / postsynaptic density
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsZhang, J. / Chang, S. / Zhang, X. / Zhu, S.
Funding supportChina , 5 items
OrganizationGrant numberCountry
National Basic Research Program of China(973 Program)2017YFA0504803China
National Basic Research Program of China(973 Program)2018YFA0507700China
National Basic Research Program of China(973 Program)2017YFA0505700China
National Natural Science Foundation of China31771115China
Chinese Academy of SciencesXDB32020000China
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 12, 2018 / Release: Jan 16, 2019

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Structure visualization

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Assembly

Deposited unit
D: Glutamate receptor ionotropic, NMDA 2A
A: Glutamate receptor ionotropic, NMDA 1
B: Glutamate receptor ionotropic, NMDA 2A
C: Glutamate receptor ionotropic, NMDA 1


Theoretical massNumber of molelcules
Total (without water)381,8804
Polyers381,8804
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)23690
ΔGint (kcal/M)-164
Surface area (Å2)164600

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Components

#1: Protein/peptide Glutamate receptor ionotropic, NMDA 2A / GluN2A / Glutamate [NMDA] receptor subunit epsilon-1 / N-methyl D-aspartate receptor subtype 2A / hNR2A


Mass: 95603.875 Da / Num. of mol.: 2 / Details: 2 mM L-Glutamate / Mutation: E656R, E657R / Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN2A, NMDAR2A / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q12879
#2: Protein/peptide Glutamate receptor ionotropic, NMDA 1 / GluN1 / Glutamate [NMDA] receptor subunit zeta-1 / N-methyl-D-aspartate receptor subunit NR1 / NMD-R1


Mass: 95336.219 Da / Num. of mol.: 2 / Details: 2 mM Glycine / Mutation: G612R / Source: (gene. exp.) Homo sapiens (human) / Gene: GRIN1, NMDAR1 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q05586

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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: Human GluN1/GluN2A NMDA receptors in the glutamate/glycine-bound state at pH 7.8
Type: COMPLEX / Details: with the presence of Glycine, L-glutamate and EDTA / Entity ID: 1, 2 / Source: RECOMBINANT
Molecular weightValue: 0.38 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Cell: HEK293S GnTI - / Organism: Homo sapiens (human) / Plasmid: pEG-Bacmam
Buffer solutionDetails: Solutions were made fresh. / pH: 7.8
Buffer component

Buffer-ID: 1

IDConc. (mg/ml)NameFormula
1150 mMsodium chlorideNaCl
220 mMHEPESC8H18N2O4S
30.05 mMEDTA(HO2CCH2)2NCH2CH2N(CH2CO2H)2
40.005 mMCholesteryl Hemisuccinate Tris SaltC31H50O4(C4H11NO3)
50.001 g/mLDigitoninC56H92O29
60.1 mMCHAPSOC32H58N2O8S
72 mMGlycineNH2CH2COOH
82 mML-Glutamic acid monosodium salt hydrateC5H8NNaO4(xH2O)
SpecimenConc.: 3.5 mg/ml / Details: Tetrameric GluN1/GluN2A NMDA receptors / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 15 mA / Grid material: GOLD / Grid mesh size: 200 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 kelvins
Details: blot for 2 seconds before plunging in liquid 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
Image recordingAverage exposure time: 8 sec. / Electron dose: 63 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4 / Num. of real images: 3171
Image scansMovie frames/image: 32 / Used frames/image: 1-32

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Processing

EM software
IDNameCategory
4GctfCTF correction
7UCSF Chimeramodel fitting
11cryoSPARCclassification
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 431818
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 131990 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-ID
14PE5A,B,C,D
25TQ0B
35H8FA,B

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