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- EMDB-16382: Transmembrane domain of resting state homomeric GluA2 F231A mutan... -

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Entry
Database: EMDB / ID: EMD-16382
TitleTransmembrane domain of resting state homomeric GluA2 F231A mutant AMPA receptor in complex with TARP gamma 2
Map data
Sample
  • Complex: homomeric GluA2 F231A mutant AMPA receptor in complex with TARP gamma 2
    • Protein or peptide: Glutamate receptor 2GRIA2
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 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


Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / neurotransmitter receptor transport, postsynaptic endosome to lysosome / LGI-ADAM interactions / Trafficking of AMPA receptors / regulation of AMPA receptor activity / neurotransmitter receptor internalization / channel regulator activity ...Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / neurotransmitter receptor transport, postsynaptic endosome to lysosome / LGI-ADAM interactions / Trafficking of AMPA receptors / regulation of AMPA receptor activity / neurotransmitter receptor internalization / channel regulator activity / membrane hyperpolarization / nervous system process / postsynaptic neurotransmitter receptor diffusion trapping / protein targeting to membrane / neurotransmitter receptor localization to postsynaptic specialization membrane / voltage-gated calcium channel complex / neuromuscular junction development / spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / transmission of nerve impulse / AMPA glutamate receptor activity / regulation of postsynaptic membrane neurotransmitter receptor levels / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / membrane depolarization / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / calcium channel regulator activity / asymmetric synapse / regulation of receptor recycling / voltage-gated calcium channel activity / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / presynaptic active zone membrane / glutamate-gated receptor activity / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / hippocampal mossy fiber to CA3 synapse / positive regulation of synaptic transmission, glutamatergic / SNARE binding / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / PDZ domain binding / protein tetramerization / postsynaptic density membrane / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / receptor internalization / terminal bouton / cerebral cortex development / synaptic vesicle membrane / response to calcium ion / synaptic vesicle / presynapse / presynaptic membrane / signaling receptor activity / amyloid-beta binding / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane
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 / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / : / Ligand-gated ion channel ...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 / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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 (rat) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhang D / Ivica J / Krieger JM / Ho H / Yamashita K / Cais O / Greger I
Funding support United Kingdom, 2 items
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, 2022-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16382.png

Downloads & links

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Map

FileDownload / File: emd_16382.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 304 pix.
= 251.104 Å		0.83 Å/pix.
x 304 pix.
= 251.104 Å		0.83 Å/pix.
x 304 pix.
= 251.104 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.024804344 - 0.045384858
Average (Standard dev.)0.00014666523 (±0.00125428)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin727272
Dimensions304304304
Spacing304304304
CellA=B=C: 251.10399 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16382_msk_1.map
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Half map: #2

Fileemd_16382_half_map_1.map
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Half map: #1

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Sample components

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Entire : homomeric GluA2 F231A mutant AMPA receptor in complex with TARP g...

EntireName: homomeric GluA2 F231A mutant AMPA receptor in complex with TARP gamma 2
Components
  • Complex: homomeric GluA2 F231A mutant AMPA receptor in complex with TARP gamma 2
    • Protein or peptide: Glutamate receptor 2GRIA2
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 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 GluA2 F231A mutant AMPA receptor in complex with TARP g...

SupramoleculeName: homomeric GluA2 F231A mutant AMPA receptor in complex with TARP gamma 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus (rat)

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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: 99.981031 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQKIMHISVL LSPVLWGLIF GDYKDDDDKV SSNSIQIGGL FPRGADQEYS AFRVGMVQFS TSEFRLTPHI DNLEVANSFA VTNAFCSQF SRGVYAIFGF YDKKSVNTIT SFCGTLHVSF ITPSFPTDGT HPFVIQMRPD LKGALLSLIE YYQWDKFAYL Y DSDRGLST ...String:
MQKIMHISVL LSPVLWGLIF GDYKDDDDKV SSNSIQIGGL FPRGADQEYS AFRVGMVQFS TSEFRLTPHI DNLEVANSFA VTNAFCSQF SRGVYAIFGF YDKKSVNTIT SFCGTLHVSF ITPSFPTDGT HPFVIQMRPD LKGALLSLIE YYQWDKFAYL Y DSDRGLST LQAVLDSAAE KKWQVTAINV GNINNDKKDE TYRSLFQDLE LKKERRVILD CERDKVNDIV DQVITIGKHV KG YHYIIAN LGFTDGDLLK IQFGGANVSG FQIVDYDDSL VSKFIERWST LEEKEYPGAH TATIKYTSAL TYDAVQVMTE AFR NLRKQR IEISRRGNAG DCLANPAVPW GQGVEIERAL KQVQVEGLSG NIKFDQNGKR INYTINIMEL KTNGPRKIGY WSEV DKMVV TLTELPSGND TSGLENKTVV VTTILESPYV MMKKNHEMLE GNERYEGYCV DLAAEIAKHC GFKYKLTIVG DGKYG ARDA DTKIWNGMVG ELVYGKADIA IAPLTITLVR EEVIDFSKPF MSLGISIMIK KPQKSKPGVF SFLDPLAYEI WMCIVF AYI GVSVVLFLVS RFSPYEWHTE EFEDGRETQS SESTNEFGIF NSLWFSLGAF MRQGCDISPR SLSGRIVGGV WWFFTLI II SSYTANLAAF LTVERMVSPI ESAEDLSKQT EIAYGTLDSG STKEFFRRSK IAVFDKMWTY MRSAEPSVFV RTTAEGVA R VRKSKGKYAY LLESTMNEYI EQRKPCDTMK VGGNLDSKGY GIATPKGSSL RTPVNLAVLK LSEQGVLDKL KNKWWYDKG ECGAKDSGSK EKTSALSLSN VAGVFYILVG GLGLAMLVAL IEFCYKSRAE AKRMKVAKNP QNINPSSSQN SQNFATYKEG YNVYGIESV KI

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: 35.807555 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLFDRGVQML LTTVGAFAAF SLMTIAVGTD YWLYSRGVCK TKSVSENETS KKNEEVMTHS GLWRTCCLEG NFKGLCKQID HFPEDADYE ADTAEYFLRA VRASSIFPIL SVILLFMGGL CIAASEFYKT RHNIILSAGI FFVSAGLSNI IGIIVYISAN A GDPSKSDS ...String:
GLFDRGVQML LTTVGAFAAF SLMTIAVGTD YWLYSRGVCK TKSVSENETS KKNEEVMTHS GLWRTCCLEG NFKGLCKQID HFPEDADYE ADTAEYFLRA VRASSIFPIL SVILLFMGGL CIAASEFYKT RHNIILSAGI FFVSAGLSNI IGIIVYISAN A GDPSKSDS KKNSYSYGWS FYFGALSFII AEMVGVLAVH MFIDRHKQLR ATARATDYLQ ASAITRIPSY RYRYQRRSRS SS RSTEPSH SRDASPVGVK GFNTLPSTEI SMYTLSRDPL KAATTPTATY NSDRDNSFLQ VHNCIQKDSK DSLHANTANR RTT PV

UniProtKB: Voltage-dependent calcium channel gamma-2 subunit

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Macromolecule #3: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 3 / Number of copies: 6 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID / 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: 4 / 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 / POPC

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 8 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 371741
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsServalcat
RefinementSpace: RECIPROCAL
Output model

PDB-8c1s:
Transmembrane domain of resting state homomeric GluA2 F231A mutant AMPA receptor in complex with TARP gamma 2

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