+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5vlo | ||||||
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タイトル | The structure of human CamKII with bound inhibitor | ||||||
要素 | Calcium/calmodulin-dependent protein kinase type II subunit delta | ||||||
キーワード | TRANSFERASE (転移酵素) / Kinase (キナーゼ) / CamKII (Ca2+/カルモジュリン依存性プロテインキナーゼII) / inhibitor (酵素阻害剤) | ||||||
機能・相同性 | 機能・相同性情報 regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / calcium- and calmodulin-dependent protein kinase complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cell communication by electrical coupling / negative regulation of sodium ion transmembrane transporter activity / Ca2+/calmodulin-dependent protein kinase / regulation of the force of heart contraction / Trafficking of AMPA receptors ...regulation of relaxation of cardiac muscle / regulation of cellular localization / negative regulation of sodium ion transmembrane transport / calcium- and calmodulin-dependent protein kinase complex / regulation of cardiac muscle cell action potential involved in regulation of contraction / regulation of cell communication by electrical coupling / negative regulation of sodium ion transmembrane transporter activity / Ca2+/calmodulin-dependent protein kinase / regulation of the force of heart contraction / Trafficking of AMPA receptors / cardiac muscle cell contraction / endoplasmic reticulum calcium ion homeostasis / Assembly and cell surface presentation of NMDA receptors / sodium channel inhibitor activity / calmodulin-dependent protein kinase activity / regulation of heart contraction / regulation of calcium ion transmembrane transport via high voltage-gated calcium channel / relaxation of cardiac muscle / CaMK IV-mediated phosphorylation of CREB / regulation of cardiac muscle cell action potential / regulation of membrane depolarization / positive regulation of cardiac muscle hypertrophy / Negative regulation of NMDA receptor-mediated neuronal transmission / positive regulation of cardiac muscle cell apoptotic process / regulation of cell communication by electrical coupling involved in cardiac conduction / Unblocking of NMDA receptors, glutamate binding and activation / Phase 0 - rapid depolarisation / regulation of heart rate by cardiac conduction / Ion transport by P-type ATPases / 長期増強 / Regulation of MECP2 expression and activity / HSF1-dependent transactivation / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / titin binding / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / sarcoplasmic reticulum membrane / cellular response to calcium ion / Ras activation upon Ca2+ influx through NMDA receptor / regulation of cell growth / peptidyl-threonine phosphorylation / RAF activation / 筋鞘 / Signaling by RAF1 mutants / endocytic vesicle membrane / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Interferon gamma signaling / Signaling by BRAF and RAF1 fusions / RAF/MAP kinase cascade / peptidyl-serine phosphorylation / transmembrane transporter binding / protein autophosphorylation / calmodulin binding / neuron projection / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / protein homodimerization activity / 核質 / ATP binding / 生体膜 / identical protein binding / 細胞核 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.05 Å | ||||||
データ登録者 | Somoza, J.R. / Villasenor, A.G. | ||||||
引用 | ジャーナル: To Be Published タイトル: Inhibitors of CamKII 著者: Somoza, T.J. / Villasenor, A.G. | ||||||
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 | 5vlo.cif.gz | 166.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5vlo.ent.gz | 107.6 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5vlo.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/vl/5vlo ftp://data.pdbj.org/pub/pdb/validation_reports/vl/5vlo | 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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2 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 34459.574 Da / 分子数: 2 / 断片: UNP residues 3-301 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CAMK2D, CAMKD / 発現宿主: Escherichia coli (大腸菌) 参照: UniProt: Q13557, Ca2+/calmodulin-dependent protein kinase #2: 化合物 | #3: 化合物 | #4: 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: 2.35 Å3/Da / 溶媒含有率: 47.64 % |
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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: CamKII S3-K301, in 20mM imidazole pH 8.5, 0.3M sodium chloride, 5mM TCEP, was concentrated to 36 mg/ml and flash frozen in liquid nitrogen for long term storage at -80 C in 10 uL aliquots. ...詳細: CamKII S3-K301, in 20mM imidazole pH 8.5, 0.3M sodium chloride, 5mM TCEP, was concentrated to 36 mg/ml and flash frozen in liquid nitrogen for long term storage at -80 C in 10 uL aliquots. The protein was thawed and diluted down to 12 mg/mL in the same buffer just prior to crystallization experiments. Sitting drop vapor diffusion droplets were assembled with 250 nL of 12 mg/mL CamKII, 0.6 mM inhibitor and 250 nL of reservoir solution 24% peg 3350, 0.2 M ammonium tartrate, 0.1 M arginine. Flat crystal plates (typically 0.03 mm x 0.2 mm x 0.4 mm in size) grew in 4-7 days at 20 C. A crystal seed suspension was prepared with ten crushed crystals combined into 100 uL of reservoir solution and stored at -80 C. A thirty fold seed dilution was prepared in the same solution for addition to protein droplets in a 1 to 1 volume ratio to enhance crystallization of difficult to crystallize inhibitors. |
-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: ALS / ビームライン: 5.0.2 / 波長: 1 Å |
検出器 | タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2016年2月25日 |
放射 | モノクロメーター: Double-crystal, Si(111) / 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: 2.05→50 Å / Num. obs: 38959 / % possible obs: 98.5 % / 冗長度: 13 % / Biso Wilson estimate: 34.660655594 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.7 |
反射 シェル | 解像度: 2.05→2.17 Å / 冗長度: 12.7 % / Mean I/σ(I) obs: 1.63 / Num. unique obs: 5733 / CC1/2: 0.742 / % possible all: 91 |
-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 / 解像度: 2.05→47.38 Å / SU ML: 0.220732142541 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 25.0433043868
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 41.0908881426 Å2 | ||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.05→47.38 Å
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拘束条件 |
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LS精密化 シェル |
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