+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6eeb | |||||||||||||||
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タイトル | Calmodulin in complex with malbrancheamide | |||||||||||||||
要素 | Calmodulin-1カルモジュリン | |||||||||||||||
キーワード | METAL BINDING PROTEIN / EF hand (EFハンド) | |||||||||||||||
機能・相同性 | 機能・相同性情報 CAM型光合成 / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation ...CAM型光合成 / Cam-PDE 1 activation / Sodium/Calcium exchangers / Calmodulin induced events / Reduction of cytosolic Ca++ levels / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / Activation of Ca-permeable Kainate Receptor / Loss of phosphorylation of MECP2 at T308 / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / negative regulation of high voltage-gated calcium channel activity / CaMK IV-mediated phosphorylation of CREB / Glycogen breakdown (glycogenolysis) / organelle localization by membrane tethering / negative regulation of calcium ion export across plasma membrane / Activation of RAC1 downstream of NMDARs / mitochondrion-endoplasmic reticulum membrane tethering / CLEC7A (Dectin-1) induces NFAT activation / regulation of cardiac muscle cell action potential / autophagosome membrane docking / positive regulation of ryanodine-sensitive calcium-release channel activity / Negative regulation of NMDA receptor-mediated neuronal transmission / regulation of cell communication by electrical coupling involved in cardiac conduction / negative regulation of peptidyl-threonine phosphorylation / Unblocking of NMDA receptors, glutamate binding and activation / Synthesis of IP3 and IP4 in the cytosol / Phase 0 - rapid depolarisation / protein phosphatase activator activity / RHO GTPases activate PAKs / positive regulation of cyclic-nucleotide phosphodiesterase activity / positive regulation of phosphoprotein phosphatase activity / Ion transport by P-type ATPases / 長期増強 / Uptake and function of anthrax toxins / Calcineurin activates NFAT / Regulation of MECP2 expression and activity / catalytic complex / DARPP-32 events / detection of calcium ion / negative regulation of ryanodine-sensitive calcium-release channel activity / Smooth Muscle Contraction / RHO GTPases activate IQGAPs / regulation of cardiac muscle contraction / calcium channel inhibitor activity / cellular response to interferon-beta / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Protein methylation / voltage-gated potassium channel complex / eNOS activation / Activation of AMPK downstream of NMDARs / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of calcium-mediated signaling / positive regulation of protein dephosphorylation / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / titin binding / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of protein autophosphorylation / sperm midpiece / calcium channel complex / substantia nigra development / adenylate cyclase activator activity / Ras activation upon Ca2+ influx through NMDA receptor / regulation of heart rate / protein serine/threonine kinase activator activity / sarcomere / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / VEGFR2 mediated vascular permeability / positive regulation of peptidyl-threonine phosphorylation / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / VEGFR2 mediated cell proliferation / regulation of cytokinesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / spindle microtubule / RAF activation / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / Transcriptional activation of mitochondrial biogenesis / Stimuli-sensing channels / 紡錘体 / cellular response to type II interferon / response to calcium ion / RAS processing / calcium-dependent protein binding / Inactivation, recovery and regulation of the phototransduction cascade / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / G2/M transition of mitotic cell cycle / Signaling by BRAF and RAF1 fusions / Platelet degranulation / 髄鞘 / Ca2+ pathway / RAF/MAP kinase cascade / vesicle / transmembrane transporter binding / Extra-nuclear estrogen signaling / G protein-coupled receptor signaling pathway 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: 1.96 Å | |||||||||||||||
データ登録者 | Beyett, T.S. / Fraley, A.E. / Tesmer, J.J.G. | |||||||||||||||
資金援助 | 米国, 4件
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引用 | ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 2019 タイトル: Perturbation of the interactions of calmodulin with GRK5 using a natural product chemical probe. 著者: Beyett, T.S. / Fraley, A.E. / Labudde, E. / Patra, D. / Coleman, R.C. / Eguchi, A. / Glukhova, A. / Chen, Q. / Williams, R.M. / Koch, W.J. / Sherman, D.H. / Tesmer, J.J.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 | 6eeb.cif.gz | 79 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6eeb.ent.gz | 56.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6eeb.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/ee/6eeb ftp://data.pdbj.org/pub/pdb/validation_reports/ee/6eeb | 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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1 |
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2 |
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単位格子 |
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Components on special symmetry positions |
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-要素
#1: タンパク質 | 分子量: 17124.805 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CALM1, CALM, CAM, CAM1 / プラスミド: pMCSG7 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P0DP23 | ||||||
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#2: 化合物 | ChemComp-J6P / ( | ||||||
#3: 化合物 | ChemComp-CA / #4: 化合物 | ChemComp-ZN / | #5: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | Y | |
-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: 2.38 Å3/Da / 溶媒含有率: 48.35 % / 解説: Rod/needle |
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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 / pH: 8.5 / 詳細: 0.1 M Tris pH 8.5, 0.2 M MgCl2, 20% (w/v) PEG 8000 / PH範囲: 8.5 |
-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: シンクロトロン / サイト: APS / ビームライン: 21-ID-D / 波長: 1.0332 Å | ||||||||||||||||||||||||||||||
検出器 | タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2018年2月20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: 1.0332 Å / 相対比: 1 | ||||||||||||||||||||||||||||||
反射 | 解像度: 1.96→38.93 Å / Num. obs: 12096 / % possible obs: 100 % / 冗長度: 13.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.057 / Rrim(I) all: 0.208 / Net I/σ(I): 7.5 | ||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1
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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: 4HEX 解像度: 1.96→37.173 Å / SU ML: 0.24 / 交差検証法: THROUGHOUT / σ(F): 1.51 / 位相誤差: 32.53
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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 max: 125.19 Å2 / Biso mean: 51.8944 Å2 / Biso min: 20.64 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 1.96→37.173 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 / Origin x: 12.3551 Å / Origin y: 64.0597 Å / Origin z: 125.1355 Å
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精密化 TLSグループ | Selection details: (chain 'A' and resid 6:147 or resid 181 or resid 201:204 ) |