+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9387 | |||||||||
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タイトル | Architecture and subunit arrangement of native AMPA receptors | |||||||||
マップデータ | Structure of a complex | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 Presynaptic depolarization and calcium channel opening / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cellular response to ammonium ion / cerebellar mossy fiber ...Presynaptic depolarization and calcium channel opening / Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cellular response to ammonium ion / cerebellar mossy fiber / neurotransmitter receptor transport, postsynaptic endosome to lysosome / LGI-ADAM interactions / myosin V binding / neurotransmitter receptor activity involved in regulation of postsynaptic cytosolic calcium ion concentration / Trafficking of AMPA receptors / neuron spine / regulation of AMPA receptor activity / neurotransmitter receptor internalization / response to arsenic-containing substance / membrane hyperpolarization / cellular response to dsRNA / postsynaptic neurotransmitter receptor diffusion trapping / nervous system process / dendritic spine membrane / Synaptic adhesion-like molecules / protein targeting to membrane / long-term synaptic depression / beta-2 adrenergic receptor binding / cellular response to peptide hormone stimulus / voltage-gated calcium channel complex / neurotransmitter receptor localization to postsynaptic specialization membrane / protein kinase A binding / neuromuscular junction development / spinal cord development / spine synapse / dendritic spine neck / neuronal cell body membrane / dendritic spine head / Activation of AMPA receptors / perisynaptic space / transmission of nerve impulse / AMPA glutamate receptor activity / channel regulator activity / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / regulation of postsynaptic membrane neurotransmitter receptor levels / immunoglobulin binding / membrane depolarization / AMPA glutamate receptor complex / adenylate cyclase binding / kainate selective glutamate receptor activity / cellular response to organic cyclic compound / ionotropic glutamate receptor complex / excitatory synapse / extracellularly glutamate-gated ion channel activity / neuronal action potential / cellular response to glycine / calcium channel regulator activity / asymmetric synapse / G-protein alpha-subunit binding / regulation of receptor recycling / voltage-gated calcium channel activity / regulation of postsynaptic membrane potential / Unblocking of NMDA receptors, glutamate binding and activation / postsynaptic density, intracellular component / positive regulation of synaptic transmission / glutamate receptor binding / long-term memory / extracellular ligand-gated monoatomic ion channel activity / positive regulation of synaptic transmission, glutamatergic / response to electrical stimulus / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / somatodendritic compartment / synapse assembly / cellular response to brain-derived neurotrophic factor stimulus / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / cytoskeletal protein binding / ionotropic glutamate receptor binding / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / hippocampal mossy fiber to CA3 synapse / cellular response to amino acid stimulus / regulation of membrane potential / SNARE binding / response to cocaine / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / long-term synaptic potentiation / protein tetramerization / postsynaptic density membrane / response to calcium ion 類似検索 - 分子機能 | |||||||||
生物種 | Rattus norvegicus (ドブネズミ) / Rat (ネズミ) / Mus musculus (ハツカネズミ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.7 Å | |||||||||
データ登録者 | Gouaux E / Zhao Y | |||||||||
引用 | ジャーナル: Science / 年: 2019 タイトル: Architecture and subunit arrangement of native AMPA receptors elucidated by cryo-EM. 著者: Yan Zhao / Shanshuang Chen / Adam C Swensen / Wei-Jun Qian / Eric Gouaux / 要旨: Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric ...Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric assemblies composed of four subunits, GluA1-GluA4. Despite decades of study, the subunit composition, subunit arrangement, and molecular structure of native AMPA receptors remain unknown. Here we elucidate the structures of 10 distinct native AMPA receptor complexes by single-particle cryo-electron microscopy (cryo-EM). We find that receptor subunits are arranged nonstochastically, with the GluA2 subunit preferentially occupying the B and D positions of the tetramer and with triheteromeric assemblies comprising a major population of native AMPA receptors. Cryo-EM maps define the structure for S2-M4 linkers between the ligand-binding and transmembrane domains, suggesting how neurotransmitter binding is coupled to ion channel gating. | |||||||||
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_9387.map.gz | 10.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9387-v30.xml emd-9387.xml | 25.6 KB 25.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_9387.png | 91.5 KB | ||
その他 | emd_9387_additional_1.map.gz emd_9387_additional_2.map.gz emd_9387_additional_3.map.gz | 7.8 MB 8.9 MB 8.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9387 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9387 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_9387_validation.pdf.gz | 314.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_9387_full_validation.pdf.gz | 314.1 KB | 表示 | |
XML形式データ | emd_9387_validation.xml.gz | 6.5 KB | 表示 | |
CIF形式データ | emd_9387_validation.cif.gz | 7.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9387 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9387 | HTTPS FTP |
-関連構造データ
関連構造データ | 6njlMC 0426C 0427C 0428C 0429C 0430C 0431C 0432C 9388C 9389C 6njmC 6njnC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ |
-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_9387.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 | Structure of a complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.72 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
-追加マップ: Structure of a complex
ファイル | emd_9387_additional_1.map | ||||||||||||
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注釈 | Structure of a complex | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Structure of a complex
ファイル | emd_9387_additional_2.map | ||||||||||||
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注釈 | Structure of a complex | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Structure of a complex
ファイル | emd_9387_additional_3.map | ||||||||||||
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注釈 | Structure of a complex | ||||||||||||
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 : Native A1A2A1A2 complex bound with MPQX
+超分子 #1: Native A1A2A1A2 complex bound with MPQX
+分子 #1: Glutamate receptor 1
+分子 #2: Glutamate receptor 2
+分子 #3: A'/C' auxiliary proteins
+分子 #4: Voltage-dependent calcium channel gamma-2 subunit
+分子 #5: 11B8 scFv
+分子 #6: 15F1 Fab light chain
+分子 #7: 15F1 Fab heavy chain
+分子 #9: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquino...
+分子 #10: 2-acetamido-2-deoxy-beta-D-glucopyranose
-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 | 4 mg/mL | ||||||||||||
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緩衝液 | pH: 8 構成要素:
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グリッド | 詳細: unspecified | ||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 295 K |
-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 K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 54.0 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 6.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION / 使用した粒子像数: 130000 |
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初期 角度割当 | タイプ: RANDOM ASSIGNMENT |
最終 角度割当 | タイプ: RANDOM ASSIGNMENT |
最終 3次元分類 | クラス数: 10 |
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
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得られたモデル | PDB-6njl: |