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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: 4il1 | ||||||
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| タイトル | Crystal Structure of the Rat Calcineurin | ||||||
要素 | Calmodulin, Calcineurin subunit B type 1, Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform | ||||||
キーワード | HYDROLASE / Calcium-binding protein / chimera protein / fusion protein / Protein phosphatase | ||||||
| 機能・相同性 | 機能・相同性情報Activation of BAD and translocation to mitochondria / Calcineurin activates NFAT / CLEC7A (Dectin-1) induces NFAT activation / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / MAP kinase serine/threonine phosphatase activity / myosin phosphatase activity / FCERI mediated Ca+2 mobilization / negative regulation of angiotensin-activated signaling pathway ...Activation of BAD and translocation to mitochondria / Calcineurin activates NFAT / CLEC7A (Dectin-1) induces NFAT activation / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / MAP kinase serine/threonine phosphatase activity / myosin phosphatase activity / FCERI mediated Ca+2 mobilization / negative regulation of angiotensin-activated signaling pathway / calcium-dependent protein serine/threonine phosphatase regulator activity / regulation of cell proliferation involved in kidney morphogenesis / regulation of store-operated calcium channel activity / positive regulation of glomerulus development / : / negative regulation of signaling / calcium-dependent protein serine/threonine phosphatase activity / positive regulation of saliva secretion / : / calmodulin-dependent protein phosphatase activity / calcineurin complex / slit diaphragm / positive regulation of connective tissue replacement / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / regulation of response to tumor cell / positive regulation of autophagic cell death / DAPK1-calmodulin complex / negative regulation of dendrite morphogenesis / positive regulation of cardiac muscle hypertrophy in response to stress / lung epithelial cell differentiation / renal filtration / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / : / : / : / : / : / calcineurin-NFAT signaling cascade / negative regulation of calcium ion-dependent exocytosis / transporter inhibitor activity / myelination in peripheral nervous system / transition between fast and slow fiber / : / type 3 metabotropic glutamate receptor binding / establishment of protein localization to membrane / positive regulation of osteoclast differentiation / Ca2+ pathway / cardiac muscle hypertrophy in response to stress / regulation of synaptic vesicle cycle / positive regulation of activated T cell proliferation / positive regulation of DNA binding / protein dephosphorylation / branching involved in blood vessel morphogenesis / dendrite morphogenesis / negative regulation of high voltage-gated calcium channel activity / protein-serine/threonine phosphatase / regulation of postsynaptic neurotransmitter receptor internalization / negative regulation of ryanodine-sensitive calcium-release channel activity / organelle localization by membrane tethering / response to corticosterone / mitochondrion-endoplasmic reticulum membrane tethering / positive regulation of cardiac muscle hypertrophy / autophagosome membrane docking / regulation of synaptic vesicle exocytosis / negative regulation of calcium ion export across plasma membrane / regulation of ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle cell action potential / presynaptic endocytosis / protein serine/threonine phosphatase activity / parallel fiber to Purkinje cell synapse / calcineurin-mediated signaling / nitric-oxide synthase binding / regulation of cell communication by electrical coupling involved in cardiac conduction / adenylate cyclase binding / protein phosphatase activator activity / epithelial to mesenchymal transition / epidermis development / regulation of synaptic vesicle endocytosis / positive regulation of osteoblast differentiation / positive regulation of endocytosis / detection of calcium ion / multicellular organismal response to stress / protein localization to nucleus / regulation of cardiac muscle contraction / postsynaptic cytosol / Schwann cell development / phosphatase binding / postsynaptic modulation of chemical synaptic transmission / cell surface receptor signaling pathway via JAK-STAT / catalytic complex / phosphatidylinositol 3-kinase binding / keratinocyte differentiation / positive regulation of nitric-oxide synthase activity / activation of adenylate cyclase activity / calcium channel inhibitor activity / presynaptic cytosol / cellular response to interferon-beta / skeletal muscle fiber development / enzyme regulator activity 類似検索 - 分子機能 | ||||||
| 生物種 | ![]() | ||||||
| 手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 3 Å | ||||||
データ登録者 | Ye, Q. / Faucher, F. / Jia, Z. | ||||||
引用 | ジャーナル: Cell Signal / 年: 2013タイトル: Structural basis of calcineurin activation by calmodulin. 著者: Ye, Q. / Feng, Y. / Yin, Y. / Faucher, F. / Currie, M.A. / Rahman, M.N. / Jin, J. / Li, S. / Wei, Q. / Jia, Z. | ||||||
| 履歴 |
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構造の表示
| 構造ビューア | 分子: Molmil Jmol/JSmol |
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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 | 4il1.cif.gz | 448.3 KB | 表示 | PDBx/mmCIF形式 |
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| PDB形式 | pdb4il1.ent.gz | 358.6 KB | 表示 | PDB形式 |
| PDBx/mmJSON形式 | 4il1.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/il/4il1 ftp://data.pdbj.org/pub/pdb/validation_reports/il/4il1 | HTTPS FTP |
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-関連構造データ
| 関連構造データ | ![]() 1mf8S S: 精密化の開始モデル |
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| 類似構造データ |
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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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| 非結晶学的対称性 (NCS) | NCSドメイン:
NCSドメイン領域: Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _
NCSアンサンブル:
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要素
| #1: タンパク質 | 分子量: 92698.812 Da / 分子数: 4 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() 遺伝子: Calm, Calm1, Calm2, Calm3, Calna, Cam, Cam1, Cam2, Cam3, Camb, Camc, Ppp3ca, Cn a2, Cnb, Ppp3r1 プラスミド: pET21a / 発現宿主: ![]() 参照: UniProt: P62161, UniProt: P63100, UniProt: P63329, UniProt: P0DP29*PLUS, protein-serine/threonine phosphatase #2: 化合物 | ChemComp-CA / #3: 水 | ChemComp-HOH / | 配列の詳細 | THE DEPOSITED PROTEIN SEQUENCE IS A CHIMERA PROTEIN: COMPOSED OF THREE PROTEINS WHICH ARE FUSED BY ...THE DEPOSITED PROTEIN SEQUENCE IS A CHIMERA PROTEIN: COMPOSED OF THREE PROTEINS WHICH ARE FUSED BY TWO GLYCINE LINKERS BETWEEN THEM. THE CLONING CONSTRUCT ORDER FOR THESE THREE PROTEINS IS CALMODULIN | |
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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: 2.8 Å3/Da / 溶媒含有率: 56.05 % |
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| 結晶化 | 温度: 293 K / pH: 5.6 詳細: PEG 3350, 1-Propanol, Citric acid, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: シンクロトロン / サイト: CHESS / ビームライン: F1 / 波長: 0.917 |
| 検出器 | タイプ: ADSC QUANTUM 270 / 検出器: CCD / 日付: 2009年5月6日 / 詳細: SYNCHROTRON OPTICS |
| 放射 | モノクロメーター: MONOCHROMATIC MACROMOLECULAR CRYSTALLOGRAPHY 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: 0.917 Å / 相対比: 1 |
| 反射 | 解像度: 3→10 Å / Num. obs: 81046 / % possible obs: 99.6 % / Observed criterion σ(I): 0 |
| 反射 シェル | 解像度: 3→3.1 Å / % possible all: 99.6 |
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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: 分子置換開始モデル: 1MF8 解像度: 3→10 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.869 / SU B: 17.535 / SU ML: 0.323 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.939 / ESU R Free: 0.385 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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| 溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 原子変位パラメータ | Biso mean: 61.91 Å2
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| 精密化ステップ | サイクル: LAST / 解像度: 3→10 Å
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| 拘束条件 |
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