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

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Entry
Database: PDB / ID: 6irf
TitleStructure of the human GluN1/GluN2A NMDA receptor in the glutamate/glycine-bound state at pH 6.3, Class I
Components
  • Glutamate receptor ionotropic, NMDA 1
  • Glutamate receptor ionotropic, NMDA 2A
KeywordsMEMBRANE PROTEIN / ionotropic glutamate receptors / NMDA receptors / synaptic protein
Function / homology
Function and homology information


excitatory chemical synaptic transmission / directional locomotion / pons maturation / response to glycine / propylene metabolic process / glutamate receptor signaling pathway / protein localization to postsynaptic membrane / serotonin metabolic process / conditioned taste aversion / olfactory learning ...excitatory chemical synaptic transmission / directional locomotion / pons maturation / response to glycine / propylene metabolic process / glutamate receptor signaling pathway / protein localization to postsynaptic membrane / serotonin metabolic process / conditioned taste aversion / olfactory learning / regulation of respiratory gaseous exchange / neurotransmitter binding / glutamate-gated calcium ion channel activity / calcium ion transmembrane import into cytosol / activation of cysteine-type endopeptidase activity / regulation of synapse assembly / NMDA glutamate receptor activity / sleep / NMDA selective glutamate receptor complex / glutamate binding / startle response / glycine binding / neurogenesis / positive regulation of cysteine-type endopeptidase activity / positive regulation of reactive oxygen species biosynthetic process / cation transport / calcium ion homeostasis / dopamine metabolic process / regulation of dendrite morphogenesis / positive regulation of calcium ion transport into cytosol / suckling behavior / male mating behavior / regulation of axonogenesis / excitatory synapse / social behavior / response to morphine / long-term memory / response to amphetamine / regulation of NMDA receptor activity / positive regulation of excitatory postsynaptic potential / excitatory postsynaptic potential / synaptic cleft / integral component of postsynaptic density membrane / long-term synaptic potentiation / prepulse inhibition / synaptic membrane / glutamate receptor activity / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / adult locomotory behavior / sensory perception of pain / ionotropic glutamate receptor signaling pathway / visual learning / synaptic transmission, glutamatergic / regulation of membrane potential / regulation of synaptic plasticity / postsynaptic density membrane / protein heterotetramerization / cerebral cortex development / regulation of long-term neuronal synaptic plasticity / memory / presynaptic membrane / terminal bouton / ephrin receptor signaling pathway / cytoplasmic vesicle membrane / negative regulation of protein catabolic process / response to wounding / modulation of chemical synaptic transmission / postsynaptic membrane / brain development / chemical synaptic transmission / synaptic vesicle / amyloid-beta binding / calmodulin binding / negative regulation of neuron apoptotic process / response to ethanol / learning or memory / dendritic spine / postsynaptic density / MAPK cascade / neuron projection / synapse / protein-containing complex binding / cell junction / positive regulation of apoptotic process / glutamatergic synapse / signaling receptor binding / dendrite / calcium ion binding / endoplasmic reticulum / integral component of plasma membrane / cell surface / positive regulation of transcription by RNA polymerase II / cell / zinc ion binding / plasma membrane / cytoplasm
Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, metazoa / Ionotropic glutamate receptor / Receptor family ligand binding region / Ligand-gated ion channel / Periplasmic binding protein-like I / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / Receptor, ligand binding region
Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsZhang, J. / Chang, S. / Zhang, X. / Zhu, S.
Funding support China, 5items
OrganizationGrant numberCountry
National Basic Research Program of China(973 Program)2017YFA0504803 China
National Basic Research Program of China(973 Program)2018YFA0507700 China
National Basic Research Program of China(973 Program)2017YFA0505700 China
National Natural Science Foundation of China31771115 China
Chinese Academy of SciencesXDBS32020000 China
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
History
DepositionNov 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: em_3d_fitting_list / pdbx_validate_close_contact ...em_3d_fitting_list / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

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  • EMDB-9715
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Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)379,0574
Polymers379,0574
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area22060 Å2
ΔGint-167 kcal/mol
Surface area152730 Å2

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Components

#1: Protein Glutamate receptor ionotropic, NMDA 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 method: isolated from a genetically manipulated source
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 Glutamate receptor ionotropic, NMDA 2A / N-methyl D-aspartate receptor subtype 2A / hNR2A


Mass: 94192.172 Da / Num. of mol.: 2 / Details: 2 mM L-Glutamate / Mutation: E656R, E657R
Source method: isolated from a genetically manipulated source
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

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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 6.3, Class I
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)Organism: Homo sapiens (human) / Cell: HEK293S GnTl- / Plasmid: pEG-Bacmam
Buffer solutionpH: 6.3 / Details: Solutions were made fresh.
Buffer component

Buffer-ID: 1

IDConc.NameFormula
1150 mMsodium chlorideNaClSodium chloride
220 mMMESC6H13NO4S
30.05 mMEDTAEthylenediaminetetraacetic acid(HO2CCH2)2NCH2CH2N(CH2CO2H)2
40.005 mMCholesteryl Hemisuccinate Tris SaltC31H50O4(C4H11NO3)
50.001 g/mLDigitoninC56H92O29
60.1 mMCHAPSOCHAPS detergentC32H58N2O8S
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 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K
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: 12 sec. / Electron dose: 56 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 4
Image scansMovie frames/image: 40 / Used frames/image: 1-40

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Processing

EM software
IDNameCategory
1Gautomatchparticle selection
4GctfCTF correction
7UCSF Chimeramodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 722287
3D reconstructionResolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 193878 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-ID
14PE5

4pe5

A
25TQ0

5tq0

B
35H8F

5h8f

A
44PE5

4pe5

B
54PE5

4pe5

C
64PE5

4pe5

D
75H8F

5h8f

B

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