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- EMDB-4572: GluA1/2 In complex with auxiliary subunit gamma-8 -

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Basic information

Entry
Database: EMDB / ID: EMD-4572
TitleGluA1/2 In complex with auxiliary subunit gamma-8
Map data
SampleGluA1/A2 bound to gamma-8
  • (Glutamate receptor ...) x 2
  • Voltage-dependent calcium channel gamma-8 subunit
  • (ligand) x 2
Function / homology
Function and homology information


Activation of AMPA receptors / Trafficking of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Cargo concentration in the ER / Synaptic adhesion-like molecules / COPII-mediated vesicle transport / cellular response to amine stimulus / positive regulation of membrane potential / neurotransmitter receptor transport, postsynaptic endosome to lysosome / L-type voltage-gated calcium channel complex ...Activation of AMPA receptors / Trafficking of AMPA receptors / Trafficking of GluR2-containing AMPA receptors / Cargo concentration in the ER / Synaptic adhesion-like molecules / COPII-mediated vesicle transport / cellular response to amine stimulus / positive regulation of membrane potential / neurotransmitter receptor transport, postsynaptic endosome to lysosome / L-type voltage-gated calcium channel complex / channel regulator activity / neurotransmitter receptor internalization / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / positive regulation of AMPA receptor activity / small GTPase binding / regulation of AMPA receptor activity / neuron spine / G-protein beta-subunit binding / myosin V binding / postsynaptic neurotransmitter receptor diffusion trapping / protein kinase A binding / neuronal action potential / cellular response to dsRNA / response to arsenic-containing substance / protein phosphatase 2B binding / calcium channel regulator activity / beta-2 adrenergic receptor binding / dendrite membrane / transmission of nerve impulse / synaptic membrane / spinal cord development / synaptic transmission, glutamatergic / postsynaptic density membrane / G-protein alpha-subunit binding / voltage-gated calcium channel activity / AMPA glutamate receptor activity / asymmetric synapse / adenylate cyclase binding / cellular response to peptide hormone stimulus / ionotropic glutamate receptor binding / long-term memory / excitatory synapse / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / response to lithium ion / regulation of receptor recycling / immunoglobulin binding / positive regulation of synaptic transmission, glutamatergic / positive regulation of synaptic transmission / response to cocaine / integral component of postsynaptic membrane / SNARE binding / response to fungicide / regulation of synaptic transmission, glutamatergic / integral component of postsynaptic density membrane / transmitter-gated ion channel activity involved in regulation of postsynaptic membrane potential / synaptic vesicle membrane / response to electrical stimulus / cellular response to amino acid stimulus / cellular response to organic cyclic compound / ionotropic glutamate receptor activity / regulation of synaptic plasticity / cellular response to growth factor stimulus / ionotropic glutamate receptor signaling pathway / cytoskeletal protein binding / response to peptide hormone / dendritic shaft / modulation of chemical synaptic transmission / response to toxic substance / Schaffer collateral - CA1 synapse / dendrite cytoplasm / receptor internalization / PDZ domain binding / integral component of presynaptic membrane / terminal bouton / presynaptic membrane / neuromuscular junction / response to organic cyclic compound / recycling endosome membrane / establishment of protein localization / postsynaptic membrane / cell-cell junction / protein tetramerization / growth cone / chemical synaptic transmission / scaffold protein binding / early endosome membrane / amyloid-beta binding / ATPase binding / response to estradiol / perikaryon / signaling receptor activity / protein C-terminus binding / early endosome / dendritic spine / postsynaptic density / cell junction / response to drug / synapse
Receptor, ligand binding region / Receptor family ligand binding region / Ionotropic glutamate receptor, metazoa / PMP-22/EMP/MP20/Claudin family / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligand-gated ion channel / Voltage-dependent calcium channel, gamma-8 subunit / Periplasmic binding protein-like I / Ionotropic glutamate receptor / PMP-22/EMP/MP20/Claudin superfamily ...Receptor, ligand binding region / Receptor family ligand binding region / Ionotropic glutamate receptor, metazoa / PMP-22/EMP/MP20/Claudin family / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligand-gated ion channel / Voltage-dependent calcium channel, gamma-8 subunit / Periplasmic binding protein-like I / Ionotropic glutamate receptor / PMP-22/EMP/MP20/Claudin superfamily / Voltage-dependent calcium channel, gamma subunit / Ligated ion channel L-glutamate- and glycine-binding site
Glutamate receptor 1 / Glutamate receptor 2 / Voltage-dependent calcium channel gamma-8 subunit
SourceRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsHerguedas B / Garcia-Nafria J / Greger IG
CitationJournal: Science / Year: 2019
Title: Architecture of the heteromeric GluA1/2 AMPA receptor in complex with the auxiliary subunit TARP γ8.
Authors: Beatriz Herguedas / Jake F Watson / Hinze Ho / Ondrej Cais / Javier García-Nafría / Ingo H Greger /
Abstract: AMPA-type glutamate receptors (AMPARs) mediate excitatory neurotransmission and are central regulators of synaptic plasticity, a molecular mechanism underlying learning and memory. Although AMPARs ...AMPA-type glutamate receptors (AMPARs) mediate excitatory neurotransmission and are central regulators of synaptic plasticity, a molecular mechanism underlying learning and memory. Although AMPARs act predominantly as heteromers, structural studies have focused on homomeric assemblies. Here, we present a cryo-electron microscopy structure of the heteromeric GluA1/2 receptor associated with two transmembrane AMPAR regulatory protein (TARP) γ8 auxiliary subunits, the principal AMPAR complex at hippocampal synapses. Within the receptor, the core subunits arrange to give the GluA2 subunit dominant control of gating. This structure reveals the geometry of the Q/R site that controls calcium flux, suggests association of TARP-stabilized lipids, and demonstrates that the extracellular loop of γ8 modulates gating by selectively interacting with the GluA2 ligand-binding domain. Collectively, this structure provides a blueprint for deciphering the signal transduction mechanisms of synaptic AMPARs.
Validation ReportPDB-ID: 6qkc

SummaryFull reportAbout validation report
DateDeposition: Jan 28, 2019 / Header (metadata) release: Mar 27, 2019 / Map release: Mar 27, 2019 / Update: May 8, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6qkc
  • Surface level: 0.03
  • 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_4572.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 220 pix.
= 308. Å
1.4 Å/pix.
x 220 pix.
= 308. Å
1.4 Å/pix.
x 220 pix.
= 308. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.070399046 - 0.12937184
Average (Standard dev.)0.00047585755 (±0.003930227)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 308.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z308.000308.000308.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-383-383-383
NX/NY/NZ768768768
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-0.0700.1290.000

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Supplemental data

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Sample components

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Entire GluA1/A2 bound to gamma-8

EntireName: GluA1/A2 bound to gamma-8 / Number of components: 6

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Component #1: protein, GluA1/A2 bound to gamma-8

ProteinName: GluA1/A2 bound to gamma-8 / Recombinant expression: No
MassTheoretical: 447 MDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Glutamate receptor 1

ProteinName: Glutamate receptor 1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 102.66193 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, Glutamate receptor 2

ProteinName: Glutamate receptor 2GRIA2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 96.247055 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, Voltage-dependent calcium channel gamma-8 subunit

ProteinName: Voltage-dependent calcium channel gamma-8 subunit / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 43.576004 kDa
SourceSpecies: Rattus norvegicus (Norway rat)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: ligand, 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxa...

LigandName: 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide
Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.33628 kDa

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Component #6: ligand, (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate

LigandName: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 0.35654 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.4 mg/mL
Buffer solution: 25 mM TRIS, pH 8, 150 mM NaCl and 0.1 % digitonin (w/v)
pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: 3uL on grid, 60 sec incubation and 4sec blotting time.

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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: 32 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -200.0 - -900.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (100.0 - 100.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5005

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C2 (2 fold cyclic) / Number of projections: 114730
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: RECIPROCAL
Input PDB model: 5WEO, 3UA8, 5KK2
Output model

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