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- EMDB-9387: structure of a complex -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-9387
Titlestructure of a complex
Map data
SampleNative A1A2A1A2 complex bound with MPQX
  • (Glutamate receptor ...) x 2
  • A'/C' auxiliary proteins
  • Voltage-dependent calcium channel gamma-2 subunit
  • 11B8 scFv
  • 15F1 Fab light chain
  • 15F1 Fab heavy chain
  • (ligand) x 2
Function / homology
Function and homology information


cellular response to amine stimulus / axonal spine / positive regulation of membrane potential / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / neurotransmitter receptor transport, postsynaptic endosome to lysosome / dendritic spine membrane / regulation of postsynaptic membrane neurotransmitter receptor levels / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / small GTPase binding ...cellular response to amine stimulus / axonal spine / positive regulation of membrane potential / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / neurotransmitter receptor transport, postsynaptic endosome to lysosome / dendritic spine membrane / regulation of postsynaptic membrane neurotransmitter receptor levels / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / small GTPase binding / positive regulation of AMPA receptor activity / cerebellar mossy fiber / regulation of AMPA receptor activity / neuron spine / neurotransmitter receptor internalization / neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic neurotransmitter receptor diffusion trapping / myosin V binding / long-term synaptic depression / membrane hyperpolarization / neuronal action potential / cellular response to dsRNA / response to arsenic-containing substance / calcium channel regulator activity / regulation of postsynaptic membrane potential / protein kinase A binding / protein targeting to membrane / voltage-gated calcium channel complex / nervous system process / beta-2 adrenergic receptor binding / transmission of nerve impulse / G-protein beta-subunit binding / neuromuscular junction development / membrane depolarization / dendrite membrane / perisynaptic space / spinal cord development / AMPA glutamate receptor activity / voltage-gated calcium channel activity / asymmetric synapse / G-protein alpha-subunit binding / ionotropic glutamate receptor binding / adenylate cyclase binding / cellular response to peptide hormone stimulus / extracellularly glutamate-gated ion channel activity / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / excitatory synapse / synaptic transmission, glutamatergic / ionotropic glutamate receptor complex / response to lithium ion / long-term memory / regulation of receptor recycling / glutamate receptor binding / immunoglobulin binding / somatodendritic compartment / positive regulation of synaptic transmission / integral component of postsynaptic density membrane / ionotropic glutamate receptor activity / regulation of synaptic transmission, glutamatergic / response to cocaine / response to fungicide / SNARE binding / cytoskeletal protein binding / response to electrical stimulus / synaptic membrane / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / response to peptide hormone / cellular response to organic cyclic compound / ionotropic glutamate receptor signaling pathway / synaptic vesicle membrane / hippocampal mossy fiber to CA3 synapse / dendritic shaft / postsynaptic density membrane / ligand-gated ion channel activity / regulation of synaptic plasticity / cellular response to amino acid stimulus / Schaffer collateral - CA1 synapse / regulation of membrane potential / integral component of presynaptic membrane / PDZ domain binding / dendrite cytoplasm / response to toxic substance / receptor internalization / modulation of chemical synaptic transmission / protein tetramerization / presynaptic membrane / neuromuscular junction / recycling endosome / terminal bouton / response to organic cyclic compound / cellular response to growth factor stimulus / establishment of protein localization / response to calcium ion / postsynapse / recycling endosome membrane / growth cone / cell-cell junction / postsynaptic membrane / chemical synaptic transmission
Receptor, ligand binding region / Ionotropic glutamate receptor / Ionotropic glutamate receptor, metazoa / Periplasmic binding protein-like I / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Voltage-dependent calcium channel, gamma subunit / Voltage-dependent calcium channel, gamma-2 subunit / PMP-22/EMP/MP20/Claudin superfamily
Glutamate receptor 1 / Glutamate receptor 2 / Voltage-dependent calcium channel gamma-2 subunit
Biological speciesRattus norvegicus (Norway rat) / Rat (rat) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsGouaux E / Zhao Y
CitationJournal: Science / Year: 2019
Title: Architecture and subunit arrangement of native AMPA receptors elucidated by cryo-EM.
Authors: Yan Zhao / Shanshuang Chen / Adam C Swensen / Wei-Jun Qian / Eric Gouaux /
Abstract: Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric ...Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric assemblies composed of four subunits, GluA1-GluA4. Despite decades of study, the subunit composition, subunit arrangement, and molecular structure of native AMPA receptors remain unknown. Here we elucidate the structures of 10 distinct native AMPA receptor complexes by single-particle cryo-electron microscopy (cryo-EM). We find that receptor subunits are arranged nonstochastically, with the GluA2 subunit preferentially occupying the B and D positions of the tetramer and with triheteromeric assemblies comprising a major population of native AMPA receptors. Cryo-EM maps define the structure for S2-M4 linkers between the ligand-binding and transmembrane domains, suggesting how neurotransmitter binding is coupled to ion channel gating.
Validation ReportPDB-ID: 6njl

SummaryFull reportAbout validation report
History
DepositionJan 3, 2019-
Header (metadata) releaseMar 6, 2019-
Map releaseApr 24, 2019-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0187
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0187
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6njl
  • Surface level: 0.0187
  • 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_9387.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.72 Å/pix.
x 320 pix.
= 550.4 Å
1.72 Å/pix.
x 320 pix.
= 550.4 Å
1.72 Å/pix.
x 320 pix.
= 550.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.72 Å
Density
Contour LevelBy AUTHOR: 0.0187 / Movie #1: 0.0187
Minimum - Maximum-0.018926315 - 0.071815446
Average (Standard dev.)0.00022293451 (±0.0022044063)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 550.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.721.721.72
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z550.400550.400550.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0190.0720.000

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Supplemental data

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Additional map: Structure of a complex

Fileemd_9387_additional_1.map
AnnotationStructure of a complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Structure of a complex

Fileemd_9387_additional_2.map
AnnotationStructure of a complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Structure of a complex

Fileemd_9387_additional_3.map
AnnotationStructure of a complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Native A1A2A1A2 complex bound with MPQX

EntireName: Native A1A2A1A2 complex bound with MPQX / Number of components: 10

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Component #1: protein, Native A1A2A1A2 complex bound with MPQX

ProteinName: Native A1A2A1A2 complex bound with MPQX / Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)

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Component #2: protein, Glutamate receptor 1

ProteinName: Glutamate receptor 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 101.518773 kDa
SourceSpecies: Rat (rat)

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Component #3: protein, Glutamate receptor 2

ProteinName: Glutamate receptor 2GRIA2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 98.783805 kDa
SourceSpecies: Rat (rat)

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Component #4: protein, A'/C' auxiliary proteins

ProteinName: A'/C' auxiliary proteins / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.039064 kDa
SourceSpecies: Rat (rat)

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Component #5: protein, Voltage-dependent calcium channel gamma-2 subunit

ProteinName: Voltage-dependent calcium channel gamma-2 subunit / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 35.938746 kDa
SourceSpecies: Rat (rat)

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Component #6: protein, 11B8 scFv

ProteinName: 11B8 scFv / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.511527 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #7: protein, 15F1 Fab light chain

ProteinName: 15F1 Fab light chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.11166 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #8: protein, 15F1 Fab heavy chain

ProteinName: 15F1 Fab heavy chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.975439 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #9: ligand, {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihy...

LigandName: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.409254 kDa

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Component #10: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 6 / 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: 8
Support filmunspecified
VitrificationCryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %

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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: 54 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 130000
3D reconstructionSoftware: RELION / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Output model

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