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- PDB-8c1q: Resting state homomeric GluA1 AMPA receptor in complex with TARP ... -

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Basic information

Entry
Database: PDB / ID: 8c1q
TitleResting state homomeric GluA1 AMPA receptor in complex with TARP gamma 3
Components
  • Glutamate receptor 1 flip isoform
  • Voltage-dependent calcium channel gamma-3 subunit
KeywordsMEMBRANE PROTEIN / AMPAR / ion channels / neurotransmission
Function / homology
Function and homology information


Cargo concentration in the ER / cellular response to ammonium ion / axonal spine / positive regulation of locomotion involved in locomotory behavior / COPII-mediated vesicle transport / positive regulation of membrane potential / response to sucrose / regulation of monoatomic ion transmembrane transport / myosin V binding / positive regulation of AMPA receptor activity ...Cargo concentration in the ER / cellular response to ammonium ion / axonal spine / positive regulation of locomotion involved in locomotory behavior / COPII-mediated vesicle transport / positive regulation of membrane potential / response to sucrose / regulation of monoatomic ion transmembrane transport / myosin V binding / positive regulation of AMPA receptor activity / LGI-ADAM interactions / neuron spine / Trafficking of AMPA receptors / postsynaptic neurotransmitter receptor diffusion trapping / proximal dendrite / response to arsenic-containing substance / regulation of AMPA receptor activity / cellular response to L-glutamate / channel regulator activity / cellular response to dsRNA / long-term synaptic depression / ligand-gated calcium channel activity / dendritic spine membrane / beta-2 adrenergic receptor binding / Synaptic adhesion-like molecules / cellular response to peptide hormone stimulus / cellular response to amine stimulus / response to morphine / response to psychosocial stress / peptide hormone receptor binding / Activation of AMPA receptors / neurotransmitter receptor localization to postsynaptic specialization membrane / perisynaptic space / spinal cord development / neuronal cell body membrane / Trafficking of GluR2-containing AMPA receptors / protein kinase A binding / response to lithium ion / AMPA glutamate receptor activity / behavioral response to pain / transmission of nerve impulse / regulation of receptor recycling / immunoglobulin binding / adenylate cyclase binding / AMPA glutamate receptor complex / response to electrical stimulus / cellular response to glycine / ionotropic glutamate receptor complex / asymmetric synapse / Unblocking of NMDA receptors, glutamate binding and activation / protein targeting / G-protein alpha-subunit binding / glutamate receptor binding / positive regulation of synaptic transmission / conditioned place preference / long-term memory / neuronal action potential / voltage-gated calcium channel activity / postsynaptic density, intracellular component / response to fungicide / glutamate-gated receptor activity / cellular response to brain-derived neurotrophic factor stimulus / positive regulation of synaptic transmission, glutamatergic / glutamate-gated calcium ion channel activity / somatodendritic compartment / synapse assembly / presynaptic active zone membrane / ionotropic glutamate receptor signaling pathway / ionotropic glutamate receptor binding / dendrite membrane / excitatory synapse / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of excitatory postsynaptic potential / cellular response to amino acid stimulus / dendritic shaft / synaptic membrane / response to cocaine / PDZ domain binding / neuromuscular junction / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / receptor internalization / cerebral cortex development / regulation of synaptic plasticity / response to nutrient levels / cellular response to growth factor stimulus / recycling endosome / postsynaptic density membrane / modulation of chemical synaptic transmission / response to toxic substance / response to peptide hormone / long-term synaptic potentiation / Schaffer collateral - CA1 synapse / small GTPase binding / recycling endosome membrane / intracellular protein localization / cell-cell junction / response to estradiol / synaptic vesicle / synaptic vesicle membrane
Similarity search - Function
Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #150 / : / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain ...Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #150 / : / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PALMITIC ACID / Chem-POV / Chem-ZK1 / Glutamate receptor 1 / Voltage-dependent calcium channel gamma-3 subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.82 Å
AuthorsZhang, D. / Ivica, J. / Krieger, J.M. / Ho, H. / Yamashita, K. / Cais, O. / Greger, I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust223194/Z/21/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105174197 United Kingdom
CitationJournal: Nature / Year: 2023
Title: Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor.
Authors: Danyang Zhang / Josip Ivica / James M Krieger / Hinze Ho / Keitaro Yamashita / Imogen Stockwell / Rozbeh Baradaran / Ondrej Cais / Ingo H Greger /
Abstract: AMPA glutamate receptors (AMPARs), the primary mediators of excitatory neurotransmission in the brain, are either GluA2 subunit-containing and thus Ca-impermeable, or GluA2-lacking and Ca-permeable. ...AMPA glutamate receptors (AMPARs), the primary mediators of excitatory neurotransmission in the brain, are either GluA2 subunit-containing and thus Ca-impermeable, or GluA2-lacking and Ca-permeable. Despite their prominent expression throughout interneurons and glia, their role in long-term potentiation and their involvement in a range of neuropathologies, structural information for GluA2-lacking receptors is currently absent. Here we determine and characterize cryo-electron microscopy structures of the GluA1 homotetramer, fully occupied with TARPγ3 auxiliary subunits (GluA1/γ3). The gating core of both resting and open-state GluA1/γ3 closely resembles GluA2-containing receptors. However, the sequence-diverse N-terminal domains (NTDs) give rise to a highly mobile assembly, enabling domain swapping and subunit re-alignments in the ligand-binding domain tier that are pronounced in desensitized states. These transitions underlie the unique kinetic properties of GluA1. A GluA2 mutant (F231A) increasing NTD dynamics phenocopies this behaviour, and exhibits reduced synaptic responses, reflecting the anchoring function of the AMPAR NTD at the synapse. Together, this work underscores how the subunit-diverse NTDs determine subunit arrangement, gating properties and ultimately synaptic signalling efficiency among AMPAR subtypes.
History
DepositionDec 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate receptor 1 flip isoform
B: Glutamate receptor 1 flip isoform
C: Glutamate receptor 1 flip isoform
D: Glutamate receptor 1 flip isoform
E: Voltage-dependent calcium channel gamma-3 subunit
F: Voltage-dependent calcium channel gamma-3 subunit
G: Voltage-dependent calcium channel gamma-3 subunit
H: Voltage-dependent calcium channel gamma-3 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)561,03826
Polymers552,3898
Non-polymers8,64918
Water45025
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

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


Mass: 102661.930 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Gria1, Glur1 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P19490
#2: Protein
Voltage-dependent calcium channel gamma-3 subunit / Neuronal voltage-gated calcium channel gamma-3 subunit / Transmembrane AMPAR regulatory protein ...Neuronal voltage-gated calcium channel gamma-3 subunit / Transmembrane AMPAR regulatory protein gamma-3 / TARP gamma-3


Mass: 35435.332 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cacng3 / Cell line (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q8VHX0

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Non-polymers , 5 types, 43 molecules

#3: Chemical
ChemComp-ZK1 / {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid / [[3,4-Dihydro-7-(4-morpholinyl)-2,3-dioxo-6-(trifluorom ethyl)-1(2H)-quinoxalinyl]methyl]phosphonic acid


Mass: 409.254 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H15F3N3O6P / Comment: medication*YM
#4: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H40O4
#6: Chemical
ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: Homomeric GluA1 AMPA receptor in complex with TARP gamma 3
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Rattus (rats)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: REFMAC / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.82 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252544 / Symmetry type: POINT
Atomic model buildingSpace: RECIPROCAL / Details: Servalcat
RefinementResolution: 2.82→2.82 Å / Cor.coef. Fo:Fc: 0.922 / SU B: 9.356 / SU ML: 0.174 / ESU R: 0.292
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.29273 --
obs0.29273 219316 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 135.112 Å2
Refinement stepCycle: 1 / Total: 18462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01218859
ELECTRON MICROSCOPYr_bond_other_d0.0010.01617953
ELECTRON MICROSCOPYr_angle_refined_deg1.4151.64725480
ELECTRON MICROSCOPYr_angle_other_deg0.5861.56541320
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.57452315
ELECTRON MICROSCOPYr_dihedral_angle_2_deg14.0542.698129
ELECTRON MICROSCOPYr_dihedral_angle_3_deg16.519102975
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0750.22825
ELECTRON MICROSCOPYr_gen_planes_refined0.0080.0221576
ELECTRON MICROSCOPYr_gen_planes_other0.0030.024428
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it14.39812.8069308
ELECTRON MICROSCOPYr_mcbond_other14.39512.8069308
ELECTRON MICROSCOPYr_mcangle_it21.63122.95611601
ELECTRON MICROSCOPYr_mcangle_other21.6322.95811602
ELECTRON MICROSCOPYr_scbond_it15.60514.3219551
ELECTRON MICROSCOPYr_scbond_other15.60414.3219552
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other25.00225.63413878
ELECTRON MICROSCOPYr_long_range_B_refined35.403150.3975183
ELECTRON MICROSCOPYr_long_range_B_other35.403150.3975184
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.79 16383 -
obs--100 %

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