+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-13970 | ||||||||||||
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タイトル | Active state of GluA1/A2 AMPA receptor in complex with TARP gamma-8 (TMD) | ||||||||||||
マップデータ | Postprocessed map of the TMD region of the complex GluA1/A2/TARP-gamma8 | ||||||||||||
試料 |
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キーワード | glutamate / AMPA receptor / TARPs / MEMBRANE PROTEIN | ||||||||||||
機能・相同性 | 機能・相同性情報 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 類似検索 - 分子機能 | ||||||||||||
生物種 | Rattus norvegicus (ドブネズミ) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.39 Å | ||||||||||||
データ登録者 | Herguedas B / Kohegyi B / Dohrke JN / Watson JF / Zhang D / Ho H / Shaikh SH / Lape R / Krieger JM / Greger IH | ||||||||||||
資金援助 | 英国, 3件
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引用 | ジャーナル: Nat Commun / 年: 2022 タイトル: Mechanisms underlying TARP modulation of the GluA1/2-γ8 AMPA receptor. 著者: 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 / 要旨: 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. | ||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_13970.map.gz | 8.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-13970-v30.xml emd-13970.xml | 21.9 KB 21.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_13970_fsc.xml | 11.4 KB | 表示 | FSCデータファイル |
画像 | emd_13970.png | 76.1 KB | ||
Filedesc metadata | emd-13970.cif.gz | 6.9 KB | ||
その他 | emd_13970_half_map_1.map.gz emd_13970_half_map_2.map.gz | 97.2 MB 97.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-13970 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13970 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_13970_validation.pdf.gz | 725.4 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_13970_full_validation.pdf.gz | 724.9 KB | 表示 | |
XML形式データ | emd_13970_validation.xml.gz | 18.6 KB | 表示 | |
CIF形式データ | emd_13970_validation.cif.gz | 24.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13970 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13970 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_13970.map.gz / 形式: CCP4 / 大きさ: 125 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Postprocessed map of the TMD region of the complex GluA1/A2/TARP-gamma8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-ハーフマップ: Half map obtained in 3D refinement with Relion
ファイル | emd_13970_half_map_1.map | ||||||||||||
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注釈 | Half map obtained in 3D refinement with Relion | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map obtained in 3D refinement with Relion
ファイル | emd_13970_half_map_2.map | ||||||||||||
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注釈 | Half map obtained in 3D refinement with Relion | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP ...
全体 | 名称: Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP gamma8 |
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要素 |
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-超分子 #1: Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP ...
超分子 | 名称: Complex between GluA1/2 AMPA receptor and auxiliary subunit TARP gamma8 タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all / 詳細: GluA2 and TARP8 are expressed as a tandem construct |
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由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) |
分子量 | 理論値: 490 KDa |
-分子 #1: AMPA Glutamate Receptor 1, isoform FLIP
分子 | 名称: AMPA Glutamate Receptor 1, isoform FLIP / タイプ: protein_or_peptide / ID: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MPYIFAFFCT GFLGAVVGAD YKDDDDKNFP NNIQIGGLFP NQQSQEHAAF RFALSQLTEP PKLLPQIDIV NISDSFEMTY RFCSQFSKGV YAIFGFYERR TVNMLTSFCG ALHVCFITPS FPVDTSNQFV LQLRPELQEA LISIIDHYKW QTFVYIYDAD RGLSVLQRVL ...文字列: 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 |
-分子 #2: AMPA Glutamate Receptor 2, isoform FLIP, Q/R edited
分子 | 名称: AMPA Glutamate Receptor 2, isoform FLIP, Q/R edited / タイプ: protein_or_peptide / ID: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIFG FYDKKSVNTI TSFCGTLHVS FITPSFPTDG THPFVIQMRP DLKGALLSLI EYYQWDKFAY LYDSDRGLST LQAVLDSAAE ...文字列: 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 |
-分子 #3: TARP gamma 8
分子 | 名称: TARP gamma 8 / タイプ: protein_or_peptide / ID: 3 / 光学異性体: LEVO |
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由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) |
組換発現 | 生物種: Homo sapiens (ヒト) |
配列 | 文字列: GESLKRWNEE RGLWCEKGVQ VLLTTIGAFA AFGLMTIAIS TDYWLYTRAL ICNTTNLTAG DDGPPHRGGS GSSEKKDPGG LTHSGLWRIC CLEGLKRGVC VKINHFPEDT DYDHDSAEYL LRVVRASSIF PILSAILLLL GGVCVAASRV YKSKRNIILG AGILFVAAGL ...文字列: 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 |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 2.5 mg/mL |
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緩衝液 | pH: 8 詳細: 25 mM TRIS 150 mM NaCl 0.02 % GDN 87 uM CTZ 100 mM L-Glu |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV / 詳細: 3-4 second blots. |
詳細 | Sample was incubated with 87 uM CTZ for 30 minutes and 100 mM L-Glutamate was added before grid preparation |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 1 / 実像数: 9664 / 平均露光時間: 4.0 sec. / 平均電子線量: 51.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: OTHER / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.2 µm / 最小 デフォーカス(公称値): 0.34 µm / 倍率(公称値): 81000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
初期モデル | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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詳細 | This map was used for guiding manual model building of the TMD region in the PDB code 7QHB (map 13969), which also contains the LBD region |
精密化 | プロトコル: RIGID BODY FIT |