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- EMDB-9156: Diheteromeric NMDA receptor GluN1/GluN2A in the 'Extended-1' conf... -

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Entry
Database: EMDB / ID: 9156
TitleDiheteromeric NMDA receptor GluN1/GluN2A in the 'Extended-1' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4
Map dataDiheteromeric NMDA receptor GluN1/GluN2A in the 'Extended-1' conformation, in complex with glycine and glutamate, in the presence of 1 micromolar zinc chloride, and at pH 7.4
SampleDiheteromeric NMDA receptor GluN1/GluN2A in the 'Extended-1' 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 / homologyEPHB-mediated forward signaling / Unblocking of NMDA receptors, glutamate binding and activation / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / N-methyl D-aspartate receptor 2B3 C-terminus / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit ...EPHB-mediated forward signaling / Unblocking of NMDA receptors, glutamate binding and activation / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Glutamate [NMDA] receptor, epsilon subunit, C-terminal / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / N-methyl D-aspartate receptor 2B3 C-terminus / Calmodulin-binding domain C0 of NMDA receptor NR1 subunit / Ionotropic glutamate receptor / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / CREB phosphorylation through the activation of CaMKII / Ras activation upon Ca2+ influx through NMDA receptor / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / Calmodulin-binding domain C0, NMDA receptor, NR1 subunit / Ionotropic glutamate receptor, metazoa / response to ammonium ion / dendritic branch / response to other organism / calcium ion transmembrane import into cytosol / cellular response to lipid / glutamate-gated calcium ion channel activity / neurotransmitter binding / ligand-gated ion channel activity involved in regulation of presynaptic membrane potential / parallel fiber to Purkinje cell synapse / action potential / cellular response to dsRNA / response to carbohydrate / glutamate receptor binding / voltage-gated cation channel activity / glycine binding / cellular response to zinc ion / NMDA glutamate receptor activity / cellular response to magnesium ion / glutamate binding / NMDA selective glutamate receptor complex / dendrite membrane / synaptic membrane / positive regulation of cysteine-type endopeptidase activity / response to methylmercury / postsynaptic density membrane / positive regulation of reactive oxygen species biosynthetic process / response to manganese ion / response to amine / spinal cord development / positive regulation of calcium ion transport into cytosol / response to light stimulus / excitatory synapse / excitatory postsynaptic potential / synaptic cleft / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / positive regulation of dendritic spine maintenance / response to cocaine / positive regulation of excitatory postsynaptic potential / phosphatase binding / integral component of postsynaptic density membrane / cerebral cortex development / response to fungicide / long-term synaptic potentiation / ionotropic glutamate receptor activity / cellular response to growth factor stimulus / ionotropic glutamate receptor signaling pathway / hippocampus development / cell adhesion molecule binding / cellular response to amino acid stimulus / cellular response to manganese ion / hippocampal mossy fiber to CA3 synapse / positive regulation of cell death / integral component of presynaptic membrane / regulation of long-term neuronal synaptic plasticity / memory / terminal bouton / presynaptic membrane / rhythmic process / protein heterotetramerization / response to calcium ion / response to organic cyclic compound / learning or memory / protein tetramerization / chemical synaptic transmission / scaffold protein binding / ATPase binding / response to ethanol / dendritic spine / postsynaptic density / protein dimerization activity / protein-containing complex binding / neuron projection / cell junction / synapse / response to drug / glutamatergic synapse / intracellular / neuronal cell body / signaling receptor binding / protein heterodimerization activity / protein kinase binding / integral component of plasma membrane
Function and homology information
SourceRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / 6.84 Å resolution
AuthorsJalali-Yazdi F / Chowdhury S / Yoshioka C / Gouaux E
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: 6mmm

SummaryFull reportAbout validation report
DateDeposition: Sep 30, 2018 / Header (metadata) release: Nov 7, 2018 / Map release: Nov 28, 2018 / Last update: Nov 28, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6mmm
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9156.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.71 Å
Density
Contour Level:4.5 (by emdb), 4.5 (movie #1):
Minimum - Maximum-13.80894 - 22.136130999999999
Average (Standard dev.)-0.000000000000342 (1.0)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin0.00.00.0
Limit191.0191.0191.0
Spacing192192192
CellA=B=C: 328.32 Å
α=β=γ: 90.0 deg.

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
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-13.80922.136-0.000

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Supplemental data

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Mask #1

Fileemd_9156_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Diheteromeric NMDA receptor GluN1/GluN2A in the 'Extended-1' conf...

EntireName: Diheteromeric NMDA receptor GluN1/GluN2A in the 'Extended-1' 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 'Extende...

ProteinName: Diheteromeric NMDA receptor GluN1/GluN2A in the 'Extended-1' 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: 40 / 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: 47299
3D reconstructionAlgorithm: FOURIER SPACE / Software: FREALIGN / Resolution: 6.84 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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