+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2i0i | ||||||
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タイトル | X-ray crystal structure of Sap97 PDZ3 bound to the C-terminal peptide of HPV18 E6 | ||||||
要素 |
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キーワード | PEPTIDE BINDING PROTEIN / Sap97 PDZ3 / HPV18 E6 / tumor suppressor (がん抑制遺伝子) / cervical carcinoma | ||||||
機能・相同性 | 機能・相同性情報 tissue morphogenesis / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / negative regulation of p38MAPK cascade ...tissue morphogenesis / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / negative regulation of p38MAPK cascade / cortical microtubule organization / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / lateral loop / reproductive structure development / myelin sheath abaxonal region / immunological synapse formation / 蠕動 / cell projection membrane / smooth muscle tissue development / paranode region of axon / bicellular tight junction assembly / Trafficking of AMPA receptors / positive regulation of potassium ion transport / ランヴィエの絞輪 / Activation of Ca-permeable Kainate Receptor / regulation of ventricular cardiac muscle cell action potential / protein-containing complex localization / establishment or maintenance of epithelial cell apical/basal polarity / amyloid precursor protein metabolic process / Synaptic adhesion-like molecules / RAF/MAP kinase cascade / neurotransmitter receptor localization to postsynaptic specialization membrane / lens development in camera-type eye / endothelial cell proliferation / ureteric bud development / regulation of myelination / cortical actin cytoskeleton organization / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / receptor clustering / 微絨毛 / kinesin binding / 免疫シナプス / 基底膜 / lateral plasma membrane / potassium channel regulator activity / Unblocking of NMDA receptors, glutamate binding and activation / bicellular tight junction / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / phosphatase binding / postsynaptic density, intracellular component / T cell proliferation / negative regulation of T cell proliferation / cellular response to brain-derived neurotrophic factor stimulus / 横行小管 / ionotropic glutamate receptor binding / T細胞 / actin filament polymerization / basal plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic membrane / regulation of membrane potential / protein localization to plasma membrane / PDZ domain binding / actin filament organization / positive regulation of protein localization to plasma membrane / postsynaptic density membrane / neuromuscular junction / protein localization / negative regulation of ERK1 and ERK2 cascade / cytoplasmic side of plasma membrane / cerebral cortex development / synaptic vesicle membrane / 細胞接着 / regulation of protein localization / negative regulation of epithelial cell proliferation / cell-cell junction / 細胞結合 / presynaptic membrane / regulation of cell shape / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / chemical synaptic transmission / basolateral plasma membrane / postsynaptic membrane / symbiont-mediated perturbation of host ubiquitin-like protein modification / 微小管 / cell population proliferation / transmembrane transporter binding / host cell cytoplasm / postsynaptic density / molecular adaptor activity / 細胞接着 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / neuron projection / 脂質ラフト / apical plasma membrane / virus-mediated perturbation of host defense response 類似検索 - 分子機能 | ||||||
生物種 | Rattus norvegicus (ドブネズミ) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 2.8 Å | ||||||
データ登録者 | Chen, X.S. / Zhang, Y. / Dasgupta, J. / Banks, L. / Thomas, M. | ||||||
引用 | ジャーナル: J.Virol. / 年: 2007 タイトル: Structures of a Human Papillomavirus (HPV) E6 Polypeptide Bound to MAGUK Proteins: Mechanisms of Targeting Tumor Suppressors by a High-Risk HPV Oncoprotein. 著者: Zhang, Y. / Dasgupta, J. / Ma, R.Z. / Banks, L. / Thomas, M. / Chen, X.S. #1: ジャーナル: Oncogene / 年: 2001 タイトル: HPV E6 and MAGUK protein interactions: determination of the molecular basis for specific protein recognition and degradation. 著者: Thomas, M. / Glaunsinger, B. / Pim, D. / Javier, R. / Banks, L. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 2i0i.cif.gz | 59.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2i0i.ent.gz | 45 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2i0i.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/i0/2i0i ftp://data.pdbj.org/pub/pdb/validation_reports/i0/2i0i | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 8776.911 Da / 分子数: 3 / 断片: PDZ3 / 由来タイプ: 組換発現 / 由来: (組換発現) Rattus norvegicus (ドブネズミ) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q62696 #2: タンパク質・ペプチド | 分子量: 947.074 Da / 分子数: 3 / 由来タイプ: 合成 詳細: The sequence of this peptide can be found in human papillomavirus type 18 (virus). 参照: UniProt: P06463 #3: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
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-試料調製
結晶 | マシュー密度: 2.39 Å3/Da / 溶媒含有率: 48.43 % |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法 / pH: 6.5 詳細: PEG4000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 291K |
-データ収集
回折 | 平均測定温度: 100 K |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU / 波長: 1.54 Å |
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 2006年5月7日 |
放射 | モノクロメーター: copper K alpha / 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: 1.54 Å / 相対比: 1 |
反射 | 解像度: 2.8→30 Å / Num. all: 6843 / Num. obs: 6381 / % possible obs: 93.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 52.9 Å2 |
-解析
ソフトウェア | 名称: CNS / バージョン: 1.1 / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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精密化 | 構造決定の手法: 分子置換 / 解像度: 2.8→19.97 Å / Rfactor Rfree error: 0.015 / Data cutoff high absF: 1594112.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 39.2021 Å2 / ksol: 0.301438 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 50.4 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.8→19.97 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.8→2.97 Å / Rfactor Rfree error: 0.064 / Total num. of bins used: 6
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Xplor file |
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