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- EMDB-17397: Homomeric GluA1 in tandem with TARP gamma-3, desensitized conform... -

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Basic information

Entry
Database: EMDB / ID: EMD-17397
TitleHomomeric GluA1 in tandem with TARP gamma-3, desensitized conformation 4
Map data
Sample
  • Complex: Homomeric GluA1 AMPA receptor in tandem with TARP gamma 3, plus 1mM quisqualate
    • Protein or peptide: Glutamate receptor 1 flip isoform
    • Protein or peptide: Voltage-dependent calcium channel gamma-3 subunit
  • Ligand: PALMITIC ACID
  • Ligand: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: water
KeywordsAMPAR / ion channels / neurotransmission / MEMBRANE PROTEIN
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
: / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / 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 / : ...: / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / 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
Similarity search - Domain/homology
Glutamate receptor 1 / Voltage-dependent calcium channel gamma-3 subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsZhang D / Krieger JM / Yamashita K / Greger I
Funding support United Kingdom, European Union, 3 items
OrganizationGrant numberCountry
Wellcome Trust223194/Z/21/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105174197 United Kingdom
H2020 Marie Curie Actions of the European Commission101024130European Union
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
DepositionMay 18, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17397.png

Downloads & links

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Map

FileDownload / File: emd_17397.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.33 Å/pix.
x 256 pix.
= 339.2 Å		1.33 Å/pix.
x 256 pix.
= 339.2 Å		1.33 Å/pix.
x 256 pix.
= 339.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.325 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.649209 - 1.201394
Average (Standard dev.)0.0009444489 (±0.04185692)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 339.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_17397_half_map_1.map
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Half map: #2

Fileemd_17397_half_map_2.map
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Sample components

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Entire : Homomeric GluA1 AMPA receptor in tandem with TARP gamma 3, plus 1...

EntireName: Homomeric GluA1 AMPA receptor in tandem with TARP gamma 3, plus 1mM quisqualate
Components
  • Complex: Homomeric GluA1 AMPA receptor in tandem with TARP gamma 3, plus 1mM quisqualate
    • Protein or peptide: Glutamate receptor 1 flip isoform
    • Protein or peptide: Voltage-dependent calcium channel gamma-3 subunit
  • Ligand: PALMITIC ACID
  • Ligand: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: water

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Supramolecule #1: Homomeric GluA1 AMPA receptor in tandem with TARP gamma 3, plus 1...

SupramoleculeName: Homomeric GluA1 AMPA receptor in tandem with TARP gamma 3, plus 1mM quisqualate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Glutamate receptor 1 flip isoform

MacromoleculeName: Glutamate receptor 1 flip isoform / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 102.66193 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPYIFAFFCT GFLGAVVGAD YKDDDDKNFP NNIQIGGLFP NQQSQEHAAF RFALSQLTEP PKLLPQIDIV NISDSFEMTY RFCSQFSKG VYAIFGFYER RTVNMLTSFC GALHVCFITP SFPVDTSNQF VLQLRPELQE ALISIIDHYK WQTFVYIYDA D RGLSVLQR ...String:
MPYIFAFFCT GFLGAVVGAD YKDDDDKNFP NNIQIGGLFP NQQSQEHAAF RFALSQLTEP PKLLPQIDIV NISDSFEMTY RFCSQFSKG VYAIFGFYER RTVNMLTSFC GALHVCFITP SFPVDTSNQF VLQLRPELQE ALISIIDHYK WQTFVYIYDA D RGLSVLQR VLDTAAEKNW QVTAVNILTT TEEGYRMLFQ DLEKKKERLV VVDCESERLN AILGQIVKLE KNGIGYHYIL AN LGFMDID LNKFKESGAN VTGFQLVNYT DTIPARIMQQ WRTSDSRDHT RVDWKRPKYT SALTYDGVKV MAEAFQSLRR QRI DISRRG NAGDCLANPA VPWGQGIDIQ RALQQVRFEG LTGNVQFNEK GRRTNYTLHV IEMKHDGIRK IGYWNEDDKF VPAA TDAQA GGDNSSVQNR TYIVTTILED PYVMLKKNAN QFEGNDRYEG YCVELAAEIA KHVGYSYRLE IVSDGKYGAR DPDTK AWNG MVGELVYGRA DVAVAPLTIT LVREEVIDFS KPFMSLGISI MIKKPQKSKP GVFSFLDPLA YEIWMCIVFA YIGVSV VLF LVSRFSPYEW HSEEFEEGRD QTTSDQSNEF GIFNSLWFSL GAFMQQGCDI SPRSLSGRIV GGVWWFFTLI IISSYTA NL AAFLTVERMV SPIESAEDLA KQTEIAYGTL EAGSTKEFFR RSKIAVFEKM WTYMKSAEPS VFVRTTEEGM IRVRKSKG K YAYLLESTMN EYIEQRKPCD TMKVGGNLDS KGYGIATPKG SALRGPVNLA VLKLSEQGVL DKLKSKWWYD KGECGSKDS GSKDKTSALS LSNVAGVFYI LIGGLGLAML VALIEFCYKS RSESKRMKGF CLIPQQSINE AIRTSTLPRN SGAGASGGGG SGENGRVVS QDFPKSMQSI PCMSHSSGMP LGATGL

UniProtKB: Glutamate receptor 1

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Macromolecule #2: Voltage-dependent calcium channel gamma-3 subunit

MacromoleculeName: Voltage-dependent calcium channel gamma-3 subunit / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 35.435332 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RMCDRGIQML ITTVGAFAAF SLMTIAVGTD YWLYSRGVCR TKSTSDNETS RKNEEVMTHS GLWRTCCLEG AFRGVCKKID HFPEDADYE QDTAEYLLRA VRASSVFPIL SVTLLFFGGL CVAASEFHRS RHSVILSAGI FFVSAGLSNI IGIIVYISAN A GDPGQRDS ...String:
RMCDRGIQML ITTVGAFAAF SLMTIAVGTD YWLYSRGVCR TKSTSDNETS RKNEEVMTHS GLWRTCCLEG AFRGVCKKID HFPEDADYE QDTAEYLLRA VRASSVFPIL SVTLLFFGGL CVAASEFHRS RHSVILSAGI FFVSAGLSNI IGIIVYISAN A GDPGQRDS KKSYSYGWSF YFGAFSFIIA EIVGVVAVHI YIEKHQQLRA RSHSELLKKS TFARLPPYRY RFRRRSSSRS TE PRSRDLS PISKGFHTIP STDISMFTLS RDPSKLTMGT LLNSDRDHAF LQFHNSTPKE FKESLHNNPA NRRTTPV

UniProtKB: Voltage-dependent calcium channel gamma-3 subunit

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Macromolecule #3: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 3 / Number of copies: 4 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #4: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate

MacromoleculeName: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / type: ligand / ID: 4 / Number of copies: 4 / Formula: OLC
Molecular weightTheoretical: 356.54 Da
Chemical component information

ChemComp-OLC:
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate

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Macromolecule #5: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 5 / Number of copies: 6 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 33 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75478
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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