+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-1761 | |||||||||
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タイトル | Single particle analysis of PSD-95 in negative stain | |||||||||
マップデータ | 3d map of PSD-95 | |||||||||
試料 |
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キーワード | Scaffold protein / Membrane associated Guanylate Kinase / PDZ / SH3 | |||||||||
機能・相同性 | 機能・相同性情報 RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization / regulation of grooming behavior / receptor localization to synapse / cellular response to potassium ion / protein localization to synapse / vocalization behavior / cerebellar mossy fiber / proximal dendrite / LGI-ADAM interactions / Trafficking of AMPA receptors / dendritic branch / neuron spine / negative regulation of receptor internalization / D1 dopamine receptor binding / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / dendritic spine morphogenesis / frizzled binding / establishment or maintenance of epithelial cell apical/basal polarity / juxtaparanode region of axon / postsynaptic neurotransmitter receptor diffusion trapping / dendritic spine organization / neuron projection terminus / acetylcholine receptor binding / positive regulation of synapse assembly / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / regulation of NMDA receptor activity / positive regulation of dendrite morphogenesis / beta-2 adrenergic receptor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / extrinsic component of cytoplasmic side of plasma membrane / locomotory exploration behavior / regulation of neuronal synaptic plasticity / kinesin binding / AMPA glutamate receptor complex / neuromuscular process controlling balance / social behavior / excitatory synapse / positive regulation of protein tyrosine kinase activity / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / positive regulation of synaptic transmission / ionotropic glutamate receptor binding / dendrite cytoplasm / synaptic membrane / cell periphery / PDZ domain binding / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / kinase binding / cerebral cortex development / cell-cell adhesion / cell-cell junction / cell junction / synaptic vesicle / positive regulation of cytosolic calcium ion concentration / scaffold protein binding / protein-containing complex assembly / basolateral plasma membrane / protein phosphatase binding / chemical synaptic transmission / postsynaptic membrane / postsynapse / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / glutamatergic synapse / dendrite / synapse / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / membrane / plasma membrane / cytosol / cytoplasm 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 / ネガティブ染色法 / 解像度: 22.9 Å | |||||||||
データ登録者 | Fomina S / Howard TD / Sleator OK / Golovanova M / O'Ryan L / Leyland M / Grossmann JG / Collins RF / Prince SM | |||||||||
引用 | ジャーナル: Biochim Biophys Acta / 年: 2011 タイトル: Self-directed assembly and clustering of the cytoplasmic domains of inwardly rectifying Kir2.1 potassium channels on association with PSD-95. 著者: Svetlana Fomina / Tina D Howard / Olivia K Sleator / Marina Golovanova / Liam O'Ryan / Mark L Leyland / J Günter Grossmann / Richard F Collins / Stephen M Prince / 要旨: The interaction of the extra-membranous domain of tetrameric inwardly rectifying Kir2.1 ion channels (Kir2.1NC(4)) with the membrane associated guanylate kinase protein PSD-95 has been studied using ...The interaction of the extra-membranous domain of tetrameric inwardly rectifying Kir2.1 ion channels (Kir2.1NC(4)) with the membrane associated guanylate kinase protein PSD-95 has been studied using Transmission Electron Microscopy in negative stain. Three types of complexes were observed in electron micrographs corresponding to a 1:1 complex, a large self-enclosed tetrad complex and extended chains of linked channel domains. Using models derived from small angle X-ray scattering experiments in which high resolution structures from X-ray crystallographic and Nuclear Magnetic Resonance studies are positioned, the envelopes from single particle analysis can be resolved as a Kir2.1NC(4):PSD-95 complex and a tetrad of this unit (Kir2.1NC(4):PSD-95)(4). The tetrad complex shows the close association of the Kir2.1 cytoplasmic domains and the influence of PSD-95 mediated self-assembly on the clustering of these channels. | |||||||||
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_1761.map.gz | 216.6 KB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-1761-v30.xml emd-1761.xml | 11.8 KB 11.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_1761.png | 91 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-1761 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1761 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_1761_validation.pdf.gz | 214.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_1761_full_validation.pdf.gz | 213.7 KB | 表示 | |
XML形式データ | emd_1761_validation.xml.gz | 4.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1761 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1761 | 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_1761.map.gz / 形式: CCP4 / 大きさ: 422.9 KB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | 3d map of PSD-95 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 3.667 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
-試料の構成要素
-全体 : Rat PSD-95
全体 | 名称: Rat PSD-95 |
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要素 |
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-超分子 #1000: Rat PSD-95
超分子 | 名称: Rat PSD-95 / タイプ: sample / ID: 1000 / 集合状態: Monomer / Number unique components: 1 |
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分子量 | 実験値: 95 KDa / 理論値: 78 KDa / 手法: SDS-PAGE |
-分子 #1: PSD-95
分子 | 名称: PSD-95 / タイプ: protein_or_peptide / ID: 1 / Name.synonym: PSD-95 / コピー数: 1 / 集合状態: Monomer / 組換発現: Yes |
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由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) / 別称: Norway Rat / 細胞中の位置: Membrane |
分子量 | 実験値: 95 KDa / 理論値: 78 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) / 組換プラスミド: pGEX-6P |
配列 | GO: neuronal ion channel clustering / InterPro: Disks large 1-like |
-実験情報
-構造解析
手法 | ネガティブ染色法 |
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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 | 1 mg/mL |
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緩衝液 | pH: 7.5 / 詳細: 20mM Tris/HCl, 5mM DTT, 1mM EDTA, |
染色 | タイプ: NEGATIVE 詳細: Samples were adsorbed onto freshly glow discharged carbon film grids. Sample solution was pipetted into the grid followed by blotting, de-ionized water was then applied for 10s followed by ...詳細: Samples were adsorbed onto freshly glow discharged carbon film grids. Sample solution was pipetted into the grid followed by blotting, de-ionized water was then applied for 10s followed by blotting, 2%w/v Uranyl Acetate solution was applied followed by a final blotting step. |
グリッド | 詳細: 400 mesh Copper |
凍結 | 凍結剤: NONE / 装置: OTHER |
-電子顕微鏡法
顕微鏡 | FEI TECNAI 10 |
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詳細 | Low dose |
撮影 | カテゴリ: FILM / フィルム・検出器のモデル: GENERIC FILM / デジタル化 - スキャナー: OTHER / デジタル化 - サンプリング間隔: 15 µm / 実像数: 2 / 詳細: none / Od range: 2 / ビット/ピクセル: 8 |
Tilt angle min | 0 |
Tilt angle max | 0 |
電子線 | 加速電圧: 100 kV / 電子線源: TUNGSTEN HAIRPIN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 3.6 mm / 最大 デフォーカス(公称値): 2.25 µm / 最小 デフォーカス(公称値): 0.9 µm / 倍率(公称値): 43000 |
試料ステージ | 試料ホルダー: Eucentric / 試料ホルダーモデル: PHILIPS ROTATION HOLDER |
-画像解析
詳細 | Particles selected using model based picking using an ab-initio model from Small angle X-ray scattering |
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CTF補正 | 詳細: Paramters determined using Scattering curve |
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 22.9 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: EMAN / 使用した粒子像数: 7854 |
最終 2次元分類 | クラス数: 84 |
-原子モデル構築 1
初期モデル | PDB ID: |
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ソフトウェア | 名称: Chimera |
詳細 | Model assembled using SAXS refinement and docked |
精密化 | 空間: REAL |
得られたモデル | PDB-2xkx: |
-原子モデル構築 2
初期モデル | PDB ID: |
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ソフトウェア | 名称: Chimera |
詳細 | Model assembled using SAXS refinement and docked |
精密化 | 空間: REAL |
得られたモデル | PDB-2xkx: |
-原子モデル構築 3
初期モデル | PDB ID: |
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ソフトウェア | 名称: Chimera |
詳細 | Model assembled using SAXS refinement and docked |
精密化 | 空間: REAL |
得られたモデル | PDB-2xkx: |