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- PDB-8c1p: Active state homomeric GluA1 AMPA receptor in complex with TARP g... -

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Basic information

Entry
Database: PDB / ID: 8c1p
TitleActive 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 / COPII-mediated vesicle transport / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / response to sucrose / regulation of monoatomic ion transmembrane transport / cellular response to L-glutamate / myosin V binding ...Cargo concentration in the ER / cellular response to ammonium ion / axonal spine / COPII-mediated vesicle transport / positive regulation of locomotion involved in locomotory behavior / positive regulation of membrane potential / response to sucrose / regulation of monoatomic ion transmembrane transport / cellular response to L-glutamate / myosin V binding / LGI-ADAM interactions / neuron spine / positive regulation of AMPA receptor activity / Trafficking of AMPA receptors / proximal dendrite / response to arsenic-containing substance / postsynaptic neurotransmitter receptor diffusion trapping / cellular response to dsRNA / regulation of AMPA receptor activity / channel regulator activity / 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 / spinal cord development / cellular response to amine stimulus / response to psychosocial stress / peptide hormone receptor binding / response to morphine / neurotransmitter receptor localization to postsynaptic specialization membrane / Activation of AMPA receptors / behavioral response to pain / perisynaptic space / neuronal cell body membrane / response to lithium ion / Trafficking of GluR2-containing AMPA receptors / protein kinase A binding / AMPA glutamate receptor activity / regulation of receptor recycling / neuronal action potential / response to electrical stimulus / adenylate cyclase binding / transmission of nerve impulse / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / cellular response to glycine / immunoglobulin binding / asymmetric synapse / Unblocking of NMDA receptors, glutamate binding and activation / G-protein alpha-subunit binding / protein targeting / glutamate receptor binding / positive regulation of synaptic transmission / conditioned place preference / long-term memory / response to fungicide / postsynaptic density, intracellular component / voltage-gated calcium channel activity / glutamate-gated receptor activity / positive regulation of synaptic transmission, glutamatergic / cellular response to brain-derived neurotrophic factor stimulus / synapse assembly / glutamate-gated calcium ion channel activity / somatodendritic compartment / presynaptic active zone membrane / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / excitatory synapse / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / cellular response to amino acid stimulus / positive regulation of excitatory postsynaptic potential / response to cocaine / dendritic shaft / synaptic membrane / neuromuscular junction / synaptic transmission, glutamatergic / PDZ domain binding / long-term synaptic potentiation / receptor internalization / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cerebral cortex development / regulation of synaptic plasticity / response to nutrient levels / response to toxic substance / recycling endosome / cellular response to growth factor stimulus / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / response to peptide hormone / small GTPase binding / intracellular protein localization / recycling endosome membrane / cell-cell junction / response to estradiol / synaptic vesicle membrane / synaptic vesicle
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
CYCLOTHIAZIDE / GLUTAMIC ACID / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / PALMITIC ACID / Chem-POV / 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: 2.9 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 16, 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)559,02228
Polymers552,3898
Non-polymers6,63320
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21A
32A
42A
53A
63A
74B
84B
95B
105B
116C
126C
137E
147E
158E
168E
179E
189E
1910F
2010F
2111F
2211F
2312G
2412G

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGOLCOLCAA - K389 - 1403415
211ARGARGOLCOLCAA - K389 - 1403415
322ARGARGOLCOLCAA - K389 - 1403415
422ARGARGOLCOLCAA - K389 - 1403415
533ARGARGOLCOLCAA - K389 - 1403415
633ARGARGOLCOLCAA - K389 - 1403415
744ARGARGPLMPLMBB - P389 - 1404415
844ARGARGPLMPLMBB - P389 - 1404415
955ARGARGPLMPLMBB - P389 - 1404415
1055ARGARGPLMPLMBB - P389 - 1404415
1166ARGARGOLCOLCCC - T389 - 1403415
1266ARGARGOLCOLCCC - T389 - 1403415
1377ASPASPPOVPOVEE - AA5 - 4014
1477ASPASPPOVPOVEE - AA5 - 4014
1588ASPASPPOVPOVEE - AA5 - 4014
1688ASPASPPOVPOVEE - AA5 - 4014
1799ASPASPPOVPOVEE - AA5 - 4014
1899ASPASPPOVPOVEE - AA5 - 4014
191010ASPASPALAALAFF5 - 2094 - 208
201010ASPASPALAALAFF5 - 2094 - 208
211111ASPASPALAALAFF5 - 2094 - 208
221111ASPASPALAALAFF5 - 2094 - 208
231212ASPASPPOVPOVGG - BA5 - 4014
241212ASPASPPOVPOVGG - BA5 - 4014

NCS ensembles :
IDDetails (eV)
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12
7Local NCS retraints between domains: 13 14
8Local NCS retraints between domains: 15 16
9Local NCS retraints between domains: 17 18
10Local NCS retraints between domains: 19 20
11Local NCS retraints between domains: 21 22
12Local NCS retraints between domains: 23 24

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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 , 6 types, 84 molecules

#3: Chemical
ChemComp-CYZ / CYCLOTHIAZIDE / 3-BICYCLO[2.2.1]HEPT-5-EN-2-YL-6-CHLORO-3,4- DIHYDRO-2H-1,2,4-BENZOTHIADIAZINE-7-SULFONAMIDE 1,1 DIOXIDE


Mass: 389.878 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H16ClN3O4S2
#4: Chemical
ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 6 / 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-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#7: Chemical ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H82NO8P / Comment: phospholipid*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: #2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 247485 / Symmetry type: POINT
Atomic model buildingSpace: RECIPROCAL / Details: Servalcat
RefinementResolution: 2.9→2.9 Å / Cor.coef. Fo:Fc: 0.877 / SU B: 7.835 / SU ML: 0.154 / ESU R: 0.239
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflection
Rwork0.3122 --
obs0.3122 276695 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 111.73 Å2
Refinement stepCycle: 1 / Total: 17849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0060.01218199
ELECTRON MICROSCOPYr_bond_other_d00.01616996
ELECTRON MICROSCOPYr_angle_refined_deg1.4141.64124667
ELECTRON MICROSCOPYr_angle_other_deg0.6241.56239078
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.65852295
ELECTRON MICROSCOPYr_dihedral_angle_2_deg4.5572.595111
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.212102692
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0870.22820
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.0221054
ELECTRON MICROSCOPYr_gen_planes_other0.0030.024338
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_it9.3911.1039252
ELECTRON MICROSCOPYr_mcbond_other9.3911.1039252
ELECTRON MICROSCOPYr_mcangle_it15.0919.91311523
ELECTRON MICROSCOPYr_mcangle_other15.08919.91511524
ELECTRON MICROSCOPYr_scbond_it10.12811.7498947
ELECTRON MICROSCOPYr_scbond_other10.12811.758948
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other16.71621.26813145
ELECTRON MICROSCOPYr_long_range_B_refined26.583125.972936
ELECTRON MICROSCOPYr_long_range_B_other26.583125.972937
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AELECTRON MICROSCOPYLocal ncs0.134450.05007
12AELECTRON MICROSCOPYLocal ncs0.134450.05007
23AELECTRON MICROSCOPYLocal ncs0.107270.05008
24AELECTRON MICROSCOPYLocal ncs0.107270.05008
35AELECTRON MICROSCOPYLocal ncs0.13610.05007
36AELECTRON MICROSCOPYLocal ncs0.13610.05007
47AELECTRON MICROSCOPYLocal ncs0.129980.05007
48AELECTRON MICROSCOPYLocal ncs0.129980.05007
59AELECTRON MICROSCOPYLocal ncs0.096340.05008
510AELECTRON MICROSCOPYLocal ncs0.096340.05008
611AELECTRON MICROSCOPYLocal ncs0.129790.05007
612AELECTRON MICROSCOPYLocal ncs0.129790.05007
713AELECTRON MICROSCOPYLocal ncs0.041650.05009
714AELECTRON MICROSCOPYLocal ncs0.041650.05009
815AELECTRON MICROSCOPYLocal ncs0.112130.05008
816AELECTRON MICROSCOPYLocal ncs0.112130.05008
917AELECTRON MICROSCOPYLocal ncs0.116050.05008
918AELECTRON MICROSCOPYLocal ncs0.116050.05008
1019AELECTRON MICROSCOPYLocal ncs0.114880.05008
1020AELECTRON MICROSCOPYLocal ncs0.114880.05008
1121AELECTRON MICROSCOPYLocal ncs0.115450.05008
1122AELECTRON MICROSCOPYLocal ncs0.115450.05008
1223AELECTRON MICROSCOPYLocal ncs0.032620.0501
1224AELECTRON MICROSCOPYLocal ncs0.032620.0501
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.831 20505 -
obs--100 %

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