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Yorodumi- EMDB-13971: Active state of GluA1/A2 AMPA receptor in complex with TARP gamma... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13971 | ||||||||||||
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Title | Active state of GluA1/A2 AMPA receptor in complex with TARP gamma-8 (LBD) | ||||||||||||
Map data | PostProcess map of the Active State of the GluA1/2/TARP8 complex (LBD only) | ||||||||||||
Sample |
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Keywords | glutamate / AMPA receptor / TARPs / MEMBRANE PROTEIN | ||||||||||||
Function / homology | Function and homology information Phase 2 - plateau phase / Phase 0 - rapid depolarisation / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / cellular response to ammonium ion / neurotransmitter receptor transport, postsynaptic endosome to lysosome / L-type voltage-gated calcium channel complex ...Phase 2 - plateau phase / Phase 0 - rapid depolarisation / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / cellular response to ammonium ion / neurotransmitter receptor transport, postsynaptic endosome to lysosome / L-type voltage-gated calcium channel complex / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / LGI-ADAM interactions / myosin V binding / Trafficking of AMPA receptors / neuron spine / regulation of AMPA receptor activity / neurotransmitter receptor internalization / channel regulator activity / protein phosphatase 2B binding / response to arsenic-containing substance / cellular response to dsRNA / postsynaptic neurotransmitter receptor diffusion trapping / dendritic spine membrane / Synaptic adhesion-like molecules / glutamate-gated calcium ion channel activity / long-term synaptic depression / cellular response to peptide hormone stimulus / protein kinase A binding / spine synapse / spinal cord development / neuronal cell body membrane / 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 / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / cellular response to organic cyclic compound / adenylate cyclase binding / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / cellular response to glycine / excitatory synapse / calcium channel regulator activity / asymmetric synapse / regulation of receptor recycling / G-protein alpha-subunit binding / voltage-gated calcium channel activity / Unblocking of NMDA receptors, glutamate binding and activation / neuronal action potential / regulation of postsynaptic membrane potential / postsynaptic density, intracellular component / glutamate receptor binding / positive regulation of synaptic transmission / long-term memory / response to electrical stimulus / glutamate-gated receptor activity / presynaptic active zone membrane / beta-2 adrenergic receptor binding / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / synapse assembly / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / positive regulation of synaptic transmission, glutamatergic / SNARE binding / response to cocaine / dendritic shaft / synaptic membrane / synaptic transmission, glutamatergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / PDZ domain binding / long-term synaptic potentiation / protein tetramerization / cellular response to amino acid stimulus / postsynaptic density membrane / ionotropic glutamate receptor binding / Schaffer collateral - CA1 synapse / modulation of chemical synaptic transmission / establishment of protein localization / regulation of synaptic plasticity / neuromuscular junction / response to organic cyclic compound / terminal bouton / receptor internalization / recycling endosome / response to toxic substance / cerebral cortex development / cellular response to growth factor stimulus Similarity search - Function | ||||||||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||||||||
Authors | Herguedas B / Kohegyi B / Dohrke JN / Watson JF / Zhang D / Ho H / Shaikh SH / Lape R / Krieger JM / Greger IH | ||||||||||||
Funding support | United Kingdom, 3 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. Authors: Beatriz Herguedas / Bianka K Kohegyi / Jan-Niklas Dohrke / Jake F Watson / Danyang Zhang / Hinze Ho / Saher A Shaikh / Remigijus Lape / James M Krieger / Ingo H Greger / Abstract: AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission at excitatory synapses in the brain. Glutamate binding to the receptor's ligand-binding domains (LBDs) leads to ion channel ...AMPA-type glutamate receptors (AMPARs) mediate rapid signal transmission at excitatory synapses in the brain. Glutamate binding to the receptor's ligand-binding domains (LBDs) leads to ion channel activation and desensitization. Gating kinetics shape synaptic transmission and are strongly modulated by transmembrane AMPAR regulatory proteins (TARPs) through currently incompletely resolved mechanisms. Here, electron cryo-microscopy structures of the GluA1/2 TARP-γ8 complex, in both open and desensitized states (at 3.5 Å), reveal state-selective engagement of the LBDs by the large TARP-γ8 loop ('β1'), elucidating how this TARP stabilizes specific gating states. We further show how TARPs alter channel rectification, by interacting with the pore helix of the selectivity filter. Lastly, we reveal that the Q/R-editing site couples the channel constriction at the filter entrance to the gate, and forms the major cation binding site in the conduction path. Our results provide a mechanistic framework of how TARPs modulate AMPAR gating and conductance. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13971.map.gz | 7.8 MB | EMDB map data format | |
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Header (meta data) | emd-13971-v30.xml emd-13971.xml | 22.2 KB 22.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13971_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_13971.png | 28.9 KB | ||
Filedesc metadata | emd-13971.cif.gz | 7 KB | ||
Others | emd_13971_half_map_1.map.gz emd_13971_half_map_2.map.gz | 97 MB 96.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13971 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13971 | HTTPS FTP |
-Validation report
Summary document | emd_13971_validation.pdf.gz | 706 KB | Display | EMDB validaton report |
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Full document | emd_13971_full_validation.pdf.gz | 705.6 KB | Display | |
Data in XML | emd_13971_validation.xml.gz | 18.5 KB | Display | |
Data in CIF | emd_13971_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13971 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13971 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13971.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | PostProcess map of the Active State of the GluA1/2/TARP8 complex (LBD only) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half map obtained in 3D refinement in Relion
File | emd_13971_half_map_1.map | ||||||||||||
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Annotation | Half map obtained in 3D refinement in Relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map obtained in 3D refinement in Relion
File | emd_13971_half_map_2.map | ||||||||||||
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Annotation | Half map obtained in 3D refinement in Relion | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP ...
Entire | Name: Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP gamma8 |
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Components |
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-Supramolecule #1: Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP ...
Supramolecule | Name: Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP gamma8 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: GluA2 and TARP8 are expressed as a tandem construct |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Molecular weight | Theoretical: 490 KDa |
-Macromolecule #1: AMPA Glutamate receptor 1, isoform Flip
Macromolecule | Name: AMPA Glutamate receptor 1, isoform Flip / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MPYIFAFFCT GFLGAVVGAD YKDDDDKNFP NNIQIGGLFP NQQSQEHAAF RFALSQLTEP PKLLPQIDIV NISDSFEMTY RFCSQFSKGV YAIFGFYERR TVNMLTSFCG ALHVCFITPS FPVDTSNQFV LQLRPELQEA LISIIDHYKW QTFVYIYDAD RGLSVLQRVL ...String: MPYIFAFFCT GFLGAVVGAD YKDDDDKNFP NNIQIGGLFP NQQSQEHAAF RFALSQLTEP PKLLPQIDIV NISDSFEMTY RFCSQFSKGV YAIFGFYERR TVNMLTSFCG ALHVCFITPS FPVDTSNQFV LQLRPELQEA LISIIDHYKW QTFVYIYDAD RGLSVLQRVL DTAAEKNWQV TAVNILTTTE EGYRMLFQDL EKKKERLVVV DCESERLNAI LGQIVKLEKN GIGYHYILAN LGFMDIDLNK FKESGANVTG FQLVNYTDTI PARIMQQWRT SDSRDHTRVD WKRPKYTSAL TYDGVKVMAE AFQSLRRQRI DISRRGNAGD CLANPAVPWG QGIDIQRALQ QVRFEGLTGN VQFNEKGRRT NYTLHVIEMK HDGIRKIGYW NEDDKFVPAA TDAQAGGDNS SVQNRTYIVT TILEDPYVML KKNANQFEGN DRYEGYCVEL AAEIAKHVGY SYRLEIVSDG KYGARDPDTK AWNGMVGELV YGRADVAVAP LTITLVREEV IDFSKPFMSL GISIMIKKPQ KSKPGVFSFL DPLAYEIWMC IVFAYIGVSV VLFLVSRFSP YEWHSEEFEE GRDQTTSDQS NEFGIFNSLW FSLGAFMQQG CDISPRSLSG RIVGGVWWFF TLIIISSYTA NLAAFLTVER MVSPIESAED LAKQTEIAYG TLEAGSTKEF FRRSKIAVFE KMWTYMKSAE PSVFVRTTEE GMIRVRKSKG KYAYLLESTM NEYIEQRKPC DTMKVGGNLD SKGYGIATPK GSALRGPVNL AVLKLSEQGV LDKLKSKWWY DKGECGSKDS GSKDKTSALS LSNVAGVFYI LIGGLGLAML VALIEFCYKS RSESKRMKGF CLIPQQSINE AIRTSTLPRN SGAGASGGGG SGENGRVVSQ DFPKSMQSIP CMSHSSGMPL GATGL |
-Macromolecule #2: AMPA Glutamate Receptor 2, isoform flip, Q/R edited
Macromolecule | Name: AMPA Glutamate Receptor 2, isoform flip, Q/R edited / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIFG FYDKKSVNTI TSFCGTLHVS FITPSFPTDG THPFVIQMRP DLKGALLSLI EYYQWDKFAY LYDSDRGLST LQAVLDSAAE ...String: MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIFG FYDKKSVNTI TSFCGTLHVS FITPSFPTDG THPFVIQMRP DLKGALLSLI EYYQWDKFAY LYDSDRGLST LQAVLDSAAE KKWQVTAINV GNINNDKKDE TYRSLFQDLE LKKERRVILD CERDKVNDIV DQVITIGKHV KGYHYIIANL GFTDGDLLKI QFGGANVSGF QIVDYDDSLV SKFIERWSTL EEKEYPGAHT ATIKYTSALT YDAVQVMTEA FRNLRKQRIE ISRRGNAGDC LANPAVPWGQ GVEIERALKQ VQVEGLSGNI KFDQNGKRIN YTINIMELKT NGPRKIGYWS EVDKMVVTLT ELPSGNDTSG LENKTVVVTT ILESPYVMMK KNHEMLEGNE RYEGYCVDLA AEIAKHCGFK YKLTIVGDGK YGARDADTKI WNGMVGELVY GKADIAIAPL TITLVREEVI DFSKPFMSLG ISIMIKKPQK SKPGVFSFLD PLAYEIWMCI VFAYIGVSVV LFLVSRFSPY EWHTEEFEDG RETQSSESTN EFGIFNSLWF SLGAFMRQGC DISPRSLSGR IVGGVWWFFT LIIISSYTAN LAAFLTVERM VSPIESAEDL SKQTEIAYGT LDSGSTKEFF RRSKIAVFDK MWTYMRSAEP SVFVRTTAEG VARVRKSKGK YAYLLESTMN EYIEQRKPCD TMKVGGNLDS KGYGIATPKG SSLGTPVNLA VLKLSEQGVL DKLKNKWWYD KGECGAKDSG SKEKTSALSL SNVAGVFYIL VGGLGLAMLV ALIEFCYKSR AEAKRMKVAK NPQNINPSSS |
-Macromolecule #3: TARP gamma 8
Macromolecule | Name: TARP gamma 8 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus norvegicus (Norway rat) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GESLKRWNEE RGLWCEKGVQ VLLTTIGAFA AFGLMTIAIS TDYWLYTRAL ICNTTNLTAG DDGPPHRGGS GSSEKKDPGG LTHSGLWRIC CLEGLKRGVC VKINHFPEDT DYDHDSAEYL LRVVRASSIF PILSAILLLL GGVCVAASRV YKSKRNIILG AGILFVAAGL ...String: GESLKRWNEE RGLWCEKGVQ VLLTTIGAFA AFGLMTIAIS TDYWLYTRAL ICNTTNLTAG DDGPPHRGGS GSSEKKDPGG LTHSGLWRIC CLEGLKRGVC VKINHFPEDT DYDHDSAEYL LRVVRASSIF PILSAILLLL GGVCVAASRV YKSKRNIILG AGILFVAAGL SNIIGVIVYI SANAGEPGPK RDEEKKNHYS YGWSFYFGGL SFILAEVIGV LAVNIYIERS REAHCQSRSD LLKAGGGAGG SGGSGPSAIL RLPSYRFRYR RRSRSSSRGS SEASPSRDAS PGGPGGPGFA STDISMYTLS RDPSKGSVAA GLASAGGGGG GAGVGAYGGA AGAAGGGGTG SERDRGSSAG FLTLHNAFPK EAASGVTVTV TGPPAAPAPA PPAPAAPAPG TLSKEAAASN TNTLNRKLEV LFQ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.5 mg/mL |
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Buffer | pH: 8 Details: 25 mM TRIS 150 mM NaCl 0.02 % GDN 87 uM CTZ 100 mM L-Glu |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3-4 second blots. |
Details | Sample was incubated with 87 uM CTZ for 30 minutes and 100 mM L-Glutamate was added before grid preparation |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9664 / Average exposure time: 4.0 sec. / Average electron dose: 51.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.34 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | This map was used for guiding manual model building of the LBD region in PDB code 7QHB (map 13969), which also contains the TMD region |
Refinement | Protocol: RIGID BODY FIT |