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- EMDB-9388: structure of a complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9388
Titlestructure of a complex
Map data
SampleNative A3A2A3A2 complex bound with MPQX
  • LBD-TMD layers of native A3A2A3A2 nAMPAR complex
  • ATD-LBD layers of native A3A2A3A2 nAMPAR complex
  • (Glutamate receptor ...) x 2
  • A'-C' auxiliary proteins
  • Voltage-dependent calcium channel gamma-2 subunit
  • 5B2 Fab Light Chain
  • 5B2 Fab Heavy Chain
  • 15F1 Fab light chain
  • 15F1 Fab heavy chain
  • (ligand) x 2
Function / homology
Function and homology information


positive regulation of protein localization to basolateral plasma membrane / eye blink reflex / neurotransmitter receptor transport, postsynaptic endosome to lysosome / regulation of postsynaptic membrane neurotransmitter receptor levels / positive regulation of AMPA receptor activity / cerebellar mossy fiber / regulation of AMPA receptor activity / neurotransmitter receptor internalization / neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic neurotransmitter receptor diffusion trapping ...positive regulation of protein localization to basolateral plasma membrane / eye blink reflex / neurotransmitter receptor transport, postsynaptic endosome to lysosome / regulation of postsynaptic membrane neurotransmitter receptor levels / positive regulation of AMPA receptor activity / cerebellar mossy fiber / regulation of AMPA receptor activity / neurotransmitter receptor internalization / neurotransmitter receptor localization to postsynaptic specialization membrane / postsynaptic neurotransmitter receptor diffusion trapping / membrane hyperpolarization / calcium channel regulator activity / protein targeting to membrane / parallel fiber to Purkinje cell synapse / voltage-gated calcium channel complex / nervous system process / transmission of nerve impulse / neuromuscular junction development / membrane depolarization / perisynaptic space / AMPA glutamate receptor activity / voltage-gated calcium channel activity / asymmetric synapse / ionotropic glutamate receptor binding / AMPA glutamate receptor complex / extracellularly glutamate-gated ion channel activity / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / response to lithium ion / regulation of receptor recycling / glutamate receptor binding / immunoglobulin binding / somatodendritic compartment / synaptic cleft / positive regulation of synaptic transmission / integral component of postsynaptic density membrane / ionotropic glutamate receptor activity / regulation of synaptic transmission, glutamatergic / response to fungicide / SNARE binding / cytoskeletal protein binding / synaptic membrane / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / ionotropic glutamate receptor signaling pathway / synaptic vesicle membrane / hippocampal mossy fiber to CA3 synapse / dendritic shaft / postsynaptic density membrane / ligand-gated ion channel activity / Schaffer collateral - CA1 synapse / regulation of membrane potential / integral component of presynaptic membrane / PDZ domain binding / dendrite cytoplasm / receptor internalization / protein tetramerization / presynaptic membrane / terminal bouton / establishment of protein localization / response to calcium ion / growth cone / postsynaptic membrane / chemical synaptic transmission / synaptic vesicle / amyloid-beta binding / ATPase binding / perikaryon / signaling receptor activity / dendritic spine / postsynaptic density / glutamatergic synapse / neuron projection / synapse / neuronal cell body / dendrite / endoplasmic reticulum membrane / protein kinase binding / endoplasmic reticulum / cell surface / integral component of plasma membrane / protein-containing complex / membrane / identical protein binding / plasma membrane / cytosol
PMP-22/EMP/MP20/Claudin superfamily / Ionotropic glutamate receptor / Ionotropic glutamate receptor, metazoa / Receptor, ligand binding region / 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
Glutamate receptor 2 / Glutamate receptor 3 / Voltage-dependent calcium channel gamma-2 subunit
Biological speciesRattus norvegicus (Norway rat) / Rat (rat) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 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: 6njm

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: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6njm
  • Surface level: 0.02
  • 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_9388.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: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.020188473 - 0.07907387
Average (Standard dev.)0.00023189404 (±0.0022921043)
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-0.0200.0790.000

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Supplemental data

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Additional map: Structure of a complex

Fileemd_9388_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_9388_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_9388_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 A3A2A3A2 complex bound with MPQX

EntireName: Native A3A2A3A2 complex bound with MPQX / Number of components: 13

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Component #1: protein, Native A3A2A3A2 complex bound with MPQX

ProteinName: Native A3A2A3A2 complex bound with MPQX / Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)

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Component #2: protein, LBD-TMD layers of native A3A2A3A2 nAMPAR complex

ProteinName: LBD-TMD layers of native A3A2A3A2 nAMPAR complex / Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)

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Component #3: protein, ATD-LBD layers of native A3A2A3A2 nAMPAR complex

ProteinName: ATD-LBD layers of native A3A2A3A2 nAMPAR complex / Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)

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Component #4: protein, Glutamate receptor 3

ProteinName: Glutamate receptor 3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 100.55668 kDa
SourceSpecies: Rat (rat)

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Component #5: 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 #6: 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 #7: 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 #8: protein, 5B2 Fab Light Chain

ProteinName: 5B2 Fab Light Chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 18.570826 kDa
SourceSpecies: Rat (rat)

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Component #9: protein, 5B2 Fab Heavy Chain

ProteinName: 5B2 Fab Heavy Chain / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 21.038842 kDa
SourceSpecies: Rat (rat)

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Component #10: 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 #11: 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 #12: 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 #13: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 4 / 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: 99000
3D reconstructionSoftware: RELION / Resolution: 6.5 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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