+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4uqj | ||||||
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タイトル | Cryo-EM density map of GluA2em in complex with ZK200775 | ||||||
要素 | GLUTAMATE RECEPTOR 2GRIA2 | ||||||
キーワード | TRANSPORT PROTEIN (運搬体タンパク質) / GLUA2EM ANTAGONIST-BOUND CLOSED STATE | ||||||
機能・相同性 | 機能・相同性情報 spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding ...spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / cytoskeletal protein binding / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / protein tetramerization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / establishment of protein localization / terminal bouton / receptor internalization / synaptic vesicle membrane / cerebral cortex development / シナプス小胞 / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / 成長円錐 / perikaryon / chemical synaptic transmission / postsynaptic membrane / scaffold protein binding / 樹状突起スパイン / postsynaptic density / neuron projection / 神経繊維 / 樹状突起 / neuronal cell body / glutamatergic synapse / シナプス / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / 細胞膜 / 小胞体 / protein-containing complex / 生体膜 / identical protein binding / 細胞膜 類似検索 - 分子機能 | ||||||
生物種 | RATTUS NORVEGICUS (ドブネズミ) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 10.4 Å | ||||||
データ登録者 | Meyerson, J.R. / Kumar, J. / Chittori, S. / Rao, P. / Pierson, J. / Bartesaghi, A. / Mayer, M.L. / Subramaniam, S. | ||||||
引用 | ジャーナル: Nature / 年: 2014 タイトル: Structural mechanism of glutamate receptor activation and desensitization. 著者: Joel R Meyerson / Janesh Kumar / Sagar Chittori / Prashant Rao / Jason Pierson / Alberto Bartesaghi / Mark L Mayer / Sriram Subramaniam / 要旨: Ionotropic glutamate receptors are ligand-gated ion channels that mediate excitatory synaptic transmission in the vertebrate brain. To gain a better understanding of how structural changes gate ion ...Ionotropic glutamate receptors are ligand-gated ion channels that mediate excitatory synaptic transmission in the vertebrate brain. To gain a better understanding of how structural changes gate ion flux across the membrane, we trapped rat AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) and kainate receptor subtypes in their major functional states and analysed the resulting structures using cryo-electron microscopy. We show that transition to the active state involves a 'corkscrew' motion of the receptor assembly, driven by closure of the ligand-binding domain. Desensitization is accompanied by disruption of the amino-terminal domain tetramer in AMPA, but not kainate, receptors with a two-fold to four-fold symmetry transition in the ligand-binding domains in both subtypes. The 7.6 Å structure of a desensitized kainate receptor shows how these changes accommodate channel closing. These findings integrate previous physiological, biochemical and structural analyses of glutamate receptors and provide a molecular explanation for key steps in receptor 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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 4uqj.cif.gz | 475.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4uqj.ent.gz | 382.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4uqj.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/uq/4uqj ftp://data.pdbj.org/pub/pdb/validation_reports/uq/4uqj | HTTPS FTP |
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-関連構造データ
関連構造データ | 2680MC 2684C 2685C 2686C 2687C 2688C 2689C 4uq6C 4uqkC 4uqqC C: 同じ文献を引用 (文献) M: このデータのモデリングに利用したマップデータ |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 92523.617 Da / 分子数: 4 / 断片: RESIDUES 22-847 / 変異: YES / 由来タイプ: 組換発現 / 由来: (組換発現) RATTUS NORVEGICUS (ドブネズミ) / 細胞株 (発現宿主): SF9 発現宿主: SPODOPTERA FRUGIPERDA (ツマジロクサヨトウ) 参照: UniProt: P19491 #2: 化合物 | ChemComp-ZK1 / {[ |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: GLUA2 / タイプ: COMPLEX |
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緩衝液 | 名称: 150 MM NACL, 20 MM TRIS, 0.75 MM DDM, 0.12 MM CHS, 0.3 MM ZK200775 pH: 8 詳細: 150 MM NACL, 20 MM TRIS, 0.75 MM DDM, 0.12 MM CHS, 0.3 MM ZK200775 |
試料 | 濃度: 1.8 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: HOLEY CARBON |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 詳細: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS / 日付: 2013年8月1日 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy / 倍率(公称値): 47000 X / 最大 デフォーカス(公称値): 3500 nm / 最小 デフォーカス(公称値): 2000 nm |
撮影 | 電子線照射量: 25 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
-解析
EMソフトウェア |
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CTF補正 | 詳細: INDIVIDUAL PARTICLES | ||||||||||||
対称性 | 点対称性: C2 (2回回転対称) | ||||||||||||
3次元再構成 | 解像度: 10.4 Å / 粒子像の数: 26795 詳細: COORDINATES FROM 3KG2 WERE FIT AS FIVE INDEPENDENT RIGID BODIES CONSISTING OF TWO ATD DIMERS AND TWO LBD DIMERS AND THE TMD. GEOMETRY AND STEREOCHEMISTRY OUTLIERS ARE THOSE PRESENT IN PDB ...詳細: COORDINATES FROM 3KG2 WERE FIT AS FIVE INDEPENDENT RIGID BODIES CONSISTING OF TWO ATD DIMERS AND TWO LBD DIMERS AND THE TMD. GEOMETRY AND STEREOCHEMISTRY OUTLIERS ARE THOSE PRESENT IN PDB 3KG2 USED FOR RIGID BODY FITS SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2680. (DEPOSITION ID: 12574). 対称性のタイプ: POINT | ||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL / 詳細: METHOD--RIGID BODY REFINEMENT PROTOCOL--X-RAY | ||||||||||||
原子モデル構築 | PDB-ID: 3KG2 | ||||||||||||
精密化 | 最高解像度: 10.4 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 10.4 Å
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