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- EMDB-9155: Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Asymme... -

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Basic information

Entry
Database: EMDB / ID: EMD-9155
TitleDiheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Asymmetric' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4
Map data
SampleDiheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Asymmetric' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4
  • (Glutamate receptor ionotropic, NMDA ...) x 2
  • ligand
Function / homology
Function and homology information


response to ammonium ion / regulation of cell communication / directional locomotion / dendritic branch / positive regulation of Schwann cell migration / response to glycine / propylene metabolic process / pons maturation / protein localization to postsynaptic membrane / locomotion ...response to ammonium ion / regulation of cell communication / directional locomotion / dendritic branch / positive regulation of Schwann cell migration / response to glycine / propylene metabolic process / pons maturation / protein localization to postsynaptic membrane / locomotion / response to other organism / serotonin metabolic process / conditioned taste aversion / olfactory learning / cellular response to lipid / regulation of respiratory gaseous exchange / neurotransmitter binding / glutamate-gated calcium ion channel activity / regulation of postsynaptic membrane potential / cellular response to dsRNA / action potential / ligand-gated ion channel activity involved in regulation of presynaptic membrane potential / calcium ion transmembrane import into cytosol / glutamate receptor binding / neuromuscular process / cellular response to zinc ion / response to carbohydrate / dendritic spine organization / voltage-gated cation channel activity / regulation of synapse assembly / NMDA glutamate receptor activity / sleep / NMDA selective glutamate receptor complex / glutamate binding / cellular response to magnesium ion / parallel fiber to Purkinje cell synapse / startle response / glycine binding / neurogenesis / regulation of neuronal synaptic plasticity / response to methylmercury / positive regulation of cysteine-type endopeptidase activity / positive regulation of reactive oxygen species biosynthetic process / dendrite membrane / response to manganese ion / regulation of neuron apoptotic process / cation transport / calcium ion homeostasis / dopamine metabolic process / response to amine / cation channel activity / regulation of dendrite morphogenesis / spinal cord development / positive regulation of calcium ion transport into cytosol / suckling behavior / male mating behavior / regulation of axonogenesis / response to light stimulus / excitatory synapse / social behavior / associative learning / response to morphine / positive regulation of dendritic spine maintenance / long-term memory / response to amphetamine / regulation of NMDA receptor activity / positive regulation of excitatory postsynaptic potential / synaptic cleft / excitatory postsynaptic potential / phosphatase binding / response to cocaine / ionotropic glutamate receptor activity / response to fungicide / integral component of postsynaptic density membrane / calcium channel activity / long-term synaptic potentiation / prepulse inhibition / synaptic membrane / glutamate receptor activity / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / sensory perception of pain / adult locomotory behavior / ionotropic glutamate receptor signaling pathway / visual learning / synaptic transmission, glutamatergic / cellular response to manganese ion / cellular response to amino acid stimulus / regulation of membrane potential / cell adhesion molecule binding / regulation of synaptic plasticity / positive regulation of cell death / cellular calcium ion homeostasis / hippocampal mossy fiber to CA3 synapse / postsynaptic density membrane / protein heterotetramerization / cerebral cortex development / hippocampus development / calcium ion transport / learning / integral component of presynaptic membrane
Ionotropic glutamate receptor / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ionotropic glutamate receptor, metazoa / Receptor, ligand binding region / Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / Periplasmic binding protein-like I
Glutamate receptor ionotropic, NMDA 1 / Glutamate receptor ionotropic, NMDA 2A
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.14 Å
AuthorsJalali-Yazdi F / Chowdhury S / Yoshioka C / Gouaux E
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS038631 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)1F32MH115595 United States
CitationJournal: Cell / Year: 2018
Title: Mechanisms for Zinc and Proton Inhibition of the GluN1/GluN2A NMDA Receptor.
Authors: Farzad Jalali-Yazdi / Sandipan Chowdhury / Craig Yoshioka / Eric Gouaux /
Abstract: N-methyl-D-aspartate receptors (NMDARs) play essential roles in memory formation, neuronal plasticity, and brain development, with their dysfunction linked to a range of disorders from ischemia to ...N-methyl-D-aspartate receptors (NMDARs) play essential roles in memory formation, neuronal plasticity, and brain development, with their dysfunction linked to a range of disorders from ischemia to schizophrenia. Zinc and pH are physiological allosteric modulators of NMDARs, with GluN2A-containing receptors inhibited by nanomolar concentrations of divalent zinc and by excursions to low pH. Despite the widespread importance of zinc and proton modulation of NMDARs, the molecular mechanism by which these ions modulate receptor activity has proven elusive. Here, we use cryoelectron microscopy to elucidate the structure of the GluN1/GluN2A NMDAR in a large ensemble of conformations under a range of physiologically relevant zinc and proton concentrations. We show how zinc binding to the amino terminal domain elicits structural changes that are transduced though the ligand-binding domain and result in constriction of the ion channel gate.
Validation ReportPDB-ID: 6mml

SummaryFull reportAbout validation report
History
DepositionSep 30, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseNov 28, 2018-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6mml
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9155.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.71 Å/pix.
x 192 pix.
= 328.32 Å
1.71 Å/pix.
x 192 pix.
= 328.32 Å
1.71 Å/pix.
x 192 pix.
= 328.32 Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.71 Å
Density
Contour LevelBy AUTHOR: 5 / Movie #1: 5
Minimum - Maximum-17.667416 - 26.565289
Average (Standard dev.)-0.00000000000 (±1)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 328.32 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.711.711.71
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z328.320328.320328.320
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-17.66726.565-0.000

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Supplemental data

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Segmentation: #1

Fileemd_9155_msk_1.map
Projections & Slices
AxesZYX

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Half map: Half-maps used for FSC calculations

Fileemd_9155_half_map_1.map
AnnotationHalf-maps used for FSC calculations
Projections & Slices
AxesZYX

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Half map: Half-maps used for FSC calculations

Fileemd_9155_half_map_2.map
AnnotationHalf-maps used for FSC calculations
Projections & Slices
AxesZYX

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Sample components

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Entire Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Asymme...

EntireName: Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Asymmetric' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4
Details: Sample was heterologously expressed in TSA-201 cells, detergent solubilized, and affinity purified
Number of components: 4

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Component #1: protein, Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuck...

ProteinName: Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Asymmetric' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4
Details: Sample was heterologously expressed in TSA-201 cells, detergent solubilized, and affinity purified
Recombinant expression: No
MassTheoretical: 500 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: TSA-201

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Component #2: protein, Glutamate receptor ionotropic, NMDA 1

ProteinName: Glutamate receptor ionotropic, NMDA 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 94.189781 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Glutamate receptor ionotropic, NMDA 2A

ProteinName: Glutamate receptor ionotropic, NMDA 2A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 93.740352 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 38 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 4 mg/mL / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 291 K / Humidity: 100 %
Details: Sample was blotted for 3 seconds at blot force 1..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 55 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 BASE (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1653

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 52489
3D reconstructionAlgorithm: FOURIER SPACE / Software: cisTEM / Resolution: 7.14 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Input PDB model: 4PE5, 5TQ0, 5I57, 5UOW
Chain ID: A, B, A, B
Output model

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