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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 7pc3 | ||||||
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タイトル | The second PDZ domain of DLG1 complexed with the PDZ-binding motif of HTLV1-TAX1 | ||||||
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![]() | PEPTIDE BINDING PROTEIN / PDZ / complex / crystallization chaperone | ||||||
機能・相同性 | ![]() regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / symbiont-mediated perturbation of host exit from mitosis / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport ...regulation of voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization / regulation of protein localization to synapse / regulation of potassium ion import / symbiont-mediated perturbation of host exit from mitosis / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / membrane raft organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / hard palate development / establishment of centrosome localization / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / negative regulation of p38MAPK cascade / guanylate kinase activity / cortical microtubule organization / regulation of sodium ion transmembrane transport / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / NrCAM interactions / lateral loop / reproductive structure development / immunological synapse formation / myelin sheath adaxonal region / myelin sheath abaxonal region / peristalsis / cell projection membrane / Synaptic adhesion-like molecules / smooth muscle tissue development / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / bicellular tight junction assembly / vesicle budding from membrane / cornified envelope / positive regulation of potassium ion transport / plasma membrane protein complex / node of Ranvier / regulation of ventricular cardiac muscle cell action potential / protein-containing complex localization / Trafficking of AMPA receptors / calcium-dependent phospholipid binding / negative regulation of receptor internalization / Assembly and cell surface presentation of NMDA receptors / establishment or maintenance of epithelial cell apical/basal polarity / collagen fibril organization / amyloid precursor protein metabolic process / Dissolution of Fibrin Clot / S100 protein binding / virion binding / neurotransmitter receptor localization to postsynaptic specialization membrane / endothelial cell proliferation / lens development in camera-type eye / positive regulation of low-density lipoprotein receptor activity / osteoclast development / epithelial cell apoptotic process / Activation of Ca-permeable Kainate Receptor / regulation of myelination / cortical actin cytoskeleton organization / establishment or maintenance of cell polarity / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of receptor recycling / positive regulation of actin filament polymerization / Negative regulation of NMDA receptor-mediated neuronal transmission / phosphatidylserine binding / Unblocking of NMDA receptors, glutamate binding and activation / receptor clustering / positive regulation of exocytosis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / phosphoprotein phosphatase activity / Long-term potentiation / immunological synapse / intercalated disc / basement membrane / regulation of neurogenesis / lateral plasma membrane / Smooth Muscle Contraction / potassium channel regulator activity / bicellular tight junction / phosphatase binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / T cell proliferation / negative regulation of T cell proliferation / fibrinolysis / cytoskeletal protein binding / phosphatidylinositol-4,5-bisphosphate binding / Ras activation upon Ca2+ influx through NMDA receptor / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / actin filament polymerization 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Cousido-Siah, A. / Trave, G. / Gogl, G. | ||||||
資金援助 | 1件
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![]() | ![]() タイトル: A scalable strategy to solve structures of PDZ domains and their complexes. 著者: Cousido-Siah, A. / Carneiro, L. / Kostmann, C. / Ecsedi, P. / Nyitray, L. / Trave, G. / Gogl, G. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 188 KB | 表示 | ![]() |
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PDB形式 | ![]() | 146.3 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 456.5 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 456.8 KB | 表示 | |
XML形式データ | ![]() | 20.2 KB | 表示 | |
CIF形式データ | ![]() | 30.8 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7pc4C ![]() 7pc5C ![]() 7pc7C ![]() 7pc8C ![]() 7pc9C ![]() 7pcbC ![]() 7qqlC ![]() 7qqmC ![]() 7qqnC ![]() 2x7zS ![]() 5n7dS S: 精密化の開始モデル C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
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集合体
登録構造単位 | ![]()
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単位格子 |
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要素
-タンパク質 / タンパク質・ペプチド , 2種, 2分子 AC
#1: タンパク質 | 分子量: 46970.566 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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#2: タンパク質・ペプチド | 分子量: 1264.363 Da / 分子数: 1 / 由来タイプ: 合成 詳細: N-terminal biotin-ttds (trioxatridecan-succinamic acid) label 由来: (合成) ![]() |
-非ポリマー , 4種, 406分子 ![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: 化合物 | ChemComp-CA / #4: 化合物 | ChemComp-GOL / #5: 化合物 | ChemComp-SO4 / | #6: 水 | ChemComp-HOH / | |
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-詳細
研究の焦点であるリガンドがあるか | N |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.62 Å3/Da / 溶媒含有率: 53.03 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 詳細: 0.2 M Lithium sulfate, 0.1 M bis-Tris pH 5.5, 25% w/v PEG 3350 |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2021年3月17日 |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 1 Å / 相対比: 1 |
反射 | 解像度: 1.95→46.553 Å / Num. obs: 36311 / % possible obs: 99.2 % / 冗長度: 13.37 % / CC1/2: 0.998 / Rrim(I) all: 0.178 / Net I/σ(I): 12.58 |
反射 シェル | 解像度: 1.95→2 Å / Mean I/σ(I) obs: 1.79 / Num. unique obs: 2616 / CC1/2: 0.645 / Rrim(I) all: 1.605 / % possible all: 98.2 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: 5N7D, 2X7Z 解像度: 1.95→46.553 Å / SU ML: 0.19 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 17.96 / 立体化学のターゲット値: ML
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溶媒の処理 | 減衰半径: 1 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 103.94 Å2 / Biso mean: 30.8243 Å2 / Biso min: 11.76 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 1.95→46.553 Å
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LS精密化 シェル | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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