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- PDB-6mmg: Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Symmet... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6mmg | ||||||||||||||||||||||||
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Title | Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Symmetric' conformation, in complex with glycine and glutamate, in the presence of 1 millimolar EDTA, and at pH 7.4 | ||||||||||||||||||||||||
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Function / homology | EPHB-mediated forward signaling / Receptor family ligand binding region / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||||||||
Specimen source | ![]() ![]() ![]() | ||||||||||||||||||||||||
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![]() | Jalali-Yazdi, F. / Chowdhury, S. / Yoshioka, C. / Gouaux, E. | ||||||||||||||||||||||||
![]() | Journal: Cell / Year: 2018 Title: Mechanisms for Zinc and Proton Inhibition of the GluN1/GluN2A NMDA Receptor. ![]() 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 Report | ![]() ![]() ![]() | ||||||||||||||||||||||||
Date | Deposition: Sep 30, 2018 / Release: Nov 28, 2018
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmcif format | ![]() ![]() |
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Links
-Related structure data
Related structure data | ![]() CM9150 ![]() C9147 ![]() C9148 ![]() C9149 ![]() C9151 ![]() C9152 ![]() C9153 ![]() C9154 ![]() C9155 ![]() C9156 ![]() C9157 ![]() C9158 ![]() C9159 ![]() C9160 ![]() C9161 ![]() C9162 ![]() C9163 ![]() C9164 ![]() C9165 ![]() C6mm9 ![]() C6mma ![]() C6mmb ![]() C6mmh ![]() C6mmi ![]() C6mmj ![]() C6mmk ![]() C6mml ![]() C6mmm ![]() C6mmn ![]() C6mmp ![]() C6mmr ![]() C6mms ![]() C6mmt ![]() C6mmu ![]() C6mmv ![]() C6mmw ![]() C6mmx C: citing same article M: map data used to model this data |
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Similar-shape strucutres |
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein/peptide | Mass: 94189.781 Da / Num. of mol.: 2 / Fragment: UNP residues 1-838 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 93740.352 Da / Num. of mol.: 2 / Fragment: UNP residues 1-837 / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / Reconstruction method: ![]() |
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Sample preparation
Component | Name: Diheteromeric NMDA receptor GluN1/GluN2A in the '2-Knuckle-Symmetric' conformation, in complex with glycine and glutamate, in the presence of 1 milliomolar EDTA, and at pH 7.4 Type: COMPLEX Details: Sample was heterologously expressed in TSA-201 cells, detergent solubilized, and affinity purified Entity ID: 1, Molecular weight | Value: 0.5 MDa / Experimental value: NO | Source (natural) | Organism: | ![]() ![]() ![]() Source (recombinant) | Cell: TSA-201 / Organism: | ![]() ![]() Buffer solution | pH: 7.4 | Buffer component |
Specimen | Conc.: 4 / Details: This sample was monodisperse / Embedding applied: NO / Shadowing applied: NO / Staining applied | ![]() ![]() Specimen support | Grid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil R1.2/1.3 | Vitrification | ![]() Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 / 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 |
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Microscopy | Microscope model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Image recording | Average exposure time: 10 / Electron dose: 55 / Film or detector model: GATAN K2 BASE (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2667 |
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Processing
Software | Name: PHENIX / Version: 1.13_2998: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 6.23 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 88979 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Ref protocol: RIGID BODY FIT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building |
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