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- PDB-6qkc: GluA1/2 In complex with auxiliary subunit gamma-8 -

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Basic information

Entry
Database: PDB / ID: 6qkc
TitleGluA1/2 In complex with auxiliary subunit gamma-8
Components
  • Glutamate receptor 1
  • Glutamate receptor 2GRIA2
  • Voltage-dependent calcium channel gamma-8 subunit
KeywordsMEMBRANE PROTEIN / AMPAR / ion channel / GluA1 / GluA2 / tarp
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
Specimen sourceRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsHerguedas, B. / Garcia-Nafria, J. / Greger, I.G.
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 Report
SummaryFull reportAbout validation report
DateDeposition: Jan 28, 2019 / Release: Mar 27, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 27, 2019Structure modelrepositoryInitial release
1.1May 8, 2019Structure modelData collection / Database referencescitation / database_PDB_rev / database_PDB_rev_record / em_admin / pdbx_database_proc_citation.journal_volume / _em_admin.last_update

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Glutamate receptor 1
B: Glutamate receptor 2
C: Glutamate receptor 1
D: Glutamate receptor 2
I: Voltage-dependent calcium channel gamma-8 subunit
J: Voltage-dependent calcium channel gamma-8 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)490,59422
Polymers484,9706
Non-polymers5,62416
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area25710 Å2
ΔGint-251 kcal/mol
Surface area95020 Å2
MethodPISA

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Components

#1: Protein/peptide Glutamate receptor 1 / / GluR-1 / AMPA-selective glutamate receptor 1 / GluR-A / GluR-K1 / Glutamate receptor ionotropic / AMPA 1 / GluA1


Mass: 102661.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria1, Glur1 / Production host: Homo sapiens (human) / References: UniProt: P19490
#2: Protein/peptide Glutamate receptor 2 / GRIA2 / GluR-2 / AMPA-selective glutamate receptor 2 / GluR-B / GluR-K2 / Glutamate receptor ionotropic / AMPA 2 / GluA2


Mass: 96247.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria2, Glur2 / Production host: Homo sapiens (human) / References: UniProt: P19491
#3: Protein/peptide Voltage-dependent calcium channel gamma-8 subunit / Neuronal voltage-gated calcium channel gamma-8 subunit / Transmembrane AMPAR regulatory protein gamma-8 / TARP gamma-8


Mass: 43576.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cacng8 / Production host: Homo sapiens (human) / References: UniProt: Q8VHW5
#4: Chemical
ChemComp-E2Q / 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide


Mass: 336.280 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H8N4O6S
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C21H40O4

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: GluA1/A2 bound to gamma-8 / Type: COMPLEX / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Molecular weightValue: 447 kDa/nm / Experimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
Details: 25 mM TRIS, pH 8, 150 mM NaCl and 0.1 % digitonin (w/v)
SpecimenConc.: 0.4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: -900 nm / Nominal defocus min: -200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µns / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 100 K
Image recordingAverage exposure time: 14 sec. / Electron dose: 32 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 3 / Num. of real images: 5005
EM imaging opticsEnergyfilter slit width: 20 eV / Phase plate: Collected using VPP
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 35

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Processing

SoftwareName: REFMAC / Version: 5.8.0236 / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4Gctf1.06CTF correction
7UCSF Chimera1.11.2model fitting
8Cootmodel fitting
10RELION3initial Euler assignment
11RELION3final Euler assignment
12RELION3classification
13RELION33D reconstruction
14REFMAC5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 114730 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
Atomic model building
IDPDB-ID3D fitting-ID
15WEO1
23UA81
35KK21
RefinementResolution: 4.1→131.6 Å / Cor.coef. Fo:Fc: 0.636 / ESU R: 3.041
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.36461 --
Obs0.36461 58500 100 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.508 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å2-1.24 Å2-0.05 Å2
2---3.18 Å20.02 Å2
3---2.31 Å2
Refinement stepCycle: 1 / Total: 13792
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0130.01314092
r_bond_other_d0.0370.01712856
r_angle_refined_deg1.3451.6519190
r_angle_other_deg2.4541.629272
r_dihedral_angle_1_deg4.70851882
r_dihedral_angle_2_deg31.22520.467428
r_dihedral_angle_3_deg17.994151776
r_dihedral_angle_4_deg10.6581546
r_chiral_restr0.1270.21950
r_gen_planes_refined0.0020.0215896
r_gen_planes_other0.0030.023140
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it4.29412.1277596
r_mcbond_other4.29612.1257587
r_mcangle_it7.87518.1679454
r_mcangle_other7.87618.1679451
r_scbond_it3.5911.4056496
r_scbond_other3.58911.4036497
r_scangle_it
r_scangle_other6.66517.2599737
r_long_range_B_refined11.51314660
r_long_range_B_other11.51314661
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 4.1→4.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.521 4260 -
Obs--100 %

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