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- EMDB-17399: Homomeric GluA2 flip R/G-edited Q/R-edited F231A mutant in tandem... -

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Basic information

Entry
Database: EMDB / ID: EMD-17399
TitleHomomeric GluA2 flip R/G-edited Q/R-edited F231A mutant in tandem with TARP gamma-2, desensitized conformation 3
Map data
Sample
  • Complex: GluA2igR_F231A-gamma2 tandem
    • Protein or peptide: Glutamate receptor 2
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 subunit
KeywordsAMPA-type glutamate neurotransmitter receptor / auxiliary subunit complex / agonist / desensitized / MEMBRANE PROTEIN
Function / homology
Function and homology information


Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / LGI-ADAM interactions / Trafficking of AMPA receptors / postsynaptic neurotransmitter receptor diffusion trapping / regulation of AMPA receptor activity / channel regulator activity / membrane hyperpolarization ...Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / LGI-ADAM interactions / Trafficking of AMPA receptors / postsynaptic neurotransmitter receptor diffusion trapping / regulation of AMPA receptor activity / channel regulator activity / membrane hyperpolarization / nervous system process / protein targeting to membrane / voltage-gated calcium channel complex / spine synapse / dendritic spine neck / dendritic spine cytoplasm / dendritic spine head / cellular response to amine stimulus / Activation of AMPA receptors / neurotransmitter receptor localization to postsynaptic specialization membrane / ligand-gated monoatomic cation channel activity / perisynaptic space / neuromuscular junction development / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor activity / AMPA glutamate receptor clustering / transmission of nerve impulse / kainate selective glutamate receptor activity / immunoglobulin binding / asymmetric synapse / AMPA glutamate receptor complex / regulation of receptor recycling / extracellularly glutamate-gated ion channel activity / cellular response to glycine / membrane depolarization / ionotropic glutamate receptor complex / Unblocking of NMDA receptors, glutamate binding and activation / conditioned place preference / glutamate receptor binding / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / voltage-gated calcium channel activity / regulation of synaptic transmission, glutamatergic / response to fungicide / positive regulation of synaptic transmission, glutamatergic / extracellular ligand-gated monoatomic ion channel activity / cytoskeletal protein binding / glutamate-gated receptor activity / cellular response to brain-derived neurotrophic factor stimulus / regulation of long-term synaptic depression / somatodendritic compartment / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / excitatory synapse / ionotropic glutamate receptor signaling pathway / ionotropic glutamate receptor binding / dendrite membrane / dendrite cytoplasm / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / dendritic shaft / SNARE binding / synaptic membrane / calcium channel regulator activity / PDZ domain binding / protein tetramerization / establishment of protein localization / synaptic transmission, glutamatergic / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cerebral cortex development / receptor internalization / response to calcium ion / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / long-term synaptic potentiation / amyloid-beta binding / synaptic vesicle membrane / growth cone / presynapse / signaling receptor activity / presynaptic membrane / scaffold protein binding / dendritic spine / chemical synaptic transmission / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / external side of plasma membrane / axon / neuronal cell body / synapse / dendrite / protein kinase binding
Similarity search - Function
Voltage-dependent calcium channel, gamma-2 subunit / : / 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 ...Voltage-dependent calcium channel, gamma-2 subunit / : / 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 2 / Voltage-dependent calcium channel gamma-2 subunit
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsKrieger JM / Zhang D / Yamashita K / Greger IH
Funding support United Kingdom, European Union, 3 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_U105174197 United Kingdom
H2020 Marie Curie Actions of the European Commission101024130European Union
Wellcome Trust223194/Z/21/Z 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
DepositionMay 18, 2023-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17399.png

Downloads & links

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Map

FileDownload / File: emd_17399.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 256 pix.
= 370.048 Å		1.45 Å/pix.
x 256 pix.
= 370.048 Å		1.45 Å/pix.
x 256 pix.
= 370.048 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4455 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.88203603 - 1.7188097
Average (Standard dev.)-0.0007814806 (±0.048385017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 370.048 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_17399_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_17399_half_map_2.map
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Sample components

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Entire : GluA2igR_F231A-gamma2 tandem

EntireName: GluA2igR_F231A-gamma2 tandem
Components
  • Complex: GluA2igR_F231A-gamma2 tandem
    • Protein or peptide: Glutamate receptor 2
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 subunit

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Supramolecule #1: GluA2igR_F231A-gamma2 tandem

SupramoleculeName: GluA2igR_F231A-gamma2 tandem / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: GluA2 C-terminus fused to gamma-2 N-terminus with a linker
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 540 KDa

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Macromolecule #1: Glutamate receptor 2

MacromoleculeName: Glutamate receptor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 98.655672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIF GFYDKKSVNT ITSFCGTLHV SFIGFPTDGT HPFVIQMRPD LKGALLSLIE YYQWDKFAYL YDSDRGLSTL Q AVLDSAAE ...String:
MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIF GFYDKKSVNT ITSFCGTLHV SFIGFPTDGT HPFVIQMRPD LKGALLSLIE YYQWDKFAYL YDSDRGLSTL Q AVLDSAAE KKWQVTAINV GNINNDKKDE TYRSLFQDLE LKKERRVILD CERDKVNDIV DQVITIGKHV KGYHYIIANL GF TDGDLLK IQFGGANVSG FQIVDYDDSL VSKFIERWST LEEKEYPGAH TATIKYTSAL TYDAVQVMTE AFRNLRKQRI EIS RRGNAG DCLANPAVPW GQGVEIERAL KQVQVEGLSG NIKFDQNGKR INYTINIMEL KTNGPRKIGY WSEVDKMVVT LTEL PSGND TSGLENKTVV VTTILESPYV MMKKNHEMLE GNERYEGYCV DLAAEIAKHC GFKYKLTIVG DGKYGARDAD TKIWN GMVG ELVYGKADIA IAPLTITLVR EEVIDFSKPF MSLGISIMIK KPQKSKPGVF SFLDPLAYEI WMCIVFAYIG VSVVLF LVS RFSPYEWHTE EFEDGRETQS SESTNEFGIF NSLWFSLGAF MRQGCDISPR SLSGRIVGGV WWFFTLIIIS SYTANLA AF LTVERMVSPI ESAEDLSKQT EIAYGTLDSG STKEFFRRSK IAVFDKMWTY MRSAEPSVFV RTTAEGVARV RKSKGKYA Y LLESTMNEYI EQRKPCDTMK VGGNLDSKGY GIATPKGSSL GTPVNLAVLK LSEQGVLDKL KNKWWYDKGE CGAKDSGSK EKTSALSLSN VAGVFYILVG GLGLAMLVAL IEFCYKSRAE AKRMKVAKNP QNINPSSSQN SQNFATYKEG YNVYGIESVK I

UniProtKB: Glutamate receptor 2

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

MacromoleculeName: Voltage-dependent calcium channel gamma-2 subunit / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 35.938746 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGLFDRGVQM LLTTVGAFAA FSLMTIAVGT DYWLYSRGVC KTKSVSENET SKKNEEVMTH SGLWRTCCLE GNFKGLCKQI DHFPEDADY EADTAEYFLR AVRASSIFPI LSVILLFMGG LCIAASEFYK TRHNIILSAG IFFVSAGLSN IIGIIVYISA N AGDPSKSD ...String:
MGLFDRGVQM LLTTVGAFAA FSLMTIAVGT DYWLYSRGVC KTKSVSENET SKKNEEVMTH SGLWRTCCLE GNFKGLCKQI DHFPEDADY EADTAEYFLR AVRASSIFPI LSVILLFMGG LCIAASEFYK TRHNIILSAG IFFVSAGLSN IIGIIVYISA N AGDPSKSD SKKNSYSYGW SFYFGALSFI IAEMVGVLAV HMFIDRHKQL RATARATDYL QASAITRIPS YRYRYQRRSR SS SRSTEPS HSRDASPVGV KGFNTLPSTE ISMYTLSRDP LKAATTPTAT YNSDRDNSFL QVHNCIQKDS KDSLHANTAN RRT TPV

UniProtKB: Voltage-dependent calcium channel gamma-2 subunit

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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: 1.4000000000000001 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: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39344
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8p3y:
Homomeric GluA2 flip R/G-edited Q/R-edited F231A mutant in tandem with TARP gamma-2, desensitized conformation 3

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