+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7t2q | ||||||
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タイトル | PEGylated Calmodulin-1 (K148U) | ||||||
要素 | Calmodulin-1カルモジュリン | ||||||
キーワード | METAL BINDING PROTEIN / Calmodulin-1 (カルモジュリン) | ||||||
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: 1.95 Å | ||||||
データ登録者 | Mackay, J.P. / Payne, R.J. / Patel, K. / Dowman, L.J. | ||||||
資金援助 | 1件
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引用 | ジャーナル: Nat Commun / 年: 2022 タイトル: Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine. 著者: Dowman, L.J. / Kulkarni, S.S. / Alegre-Requena, J.V. / Giltrap, A.M. / Norman, A.R. / Sharma, A. / Gallegos, L.C. / Mackay, A.S. / Welegedara, A.P. / Watson, E.E. / van Raad, D. / ...著者: Dowman, L.J. / Kulkarni, S.S. / Alegre-Requena, J.V. / Giltrap, A.M. / Norman, A.R. / Sharma, A. / Gallegos, L.C. / Mackay, A.S. / Welegedara, A.P. / Watson, E.E. / van Raad, D. / Niederacher, G. / Huhmann, S. / Proschogo, N. / Patel, K. / Larance, M. / Becker, C.F.W. / Mackay, J.P. / Lakhwani, G. / Huber, T. / Paton, R.S. / Payne, R.J. | ||||||
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 | 7t2q.cif.gz | 54.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7t2q.ent.gz | 31.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7t2q.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/t2/7t2q ftp://data.pdbj.org/pub/pdb/validation_reports/t2/7t2q | HTTPS FTP |
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-関連構造データ
関連構造データ | 6eebS S: 精密化の開始モデル |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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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Components on special symmetry positions |
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-要素
#1: タンパク質 | 分子量: 16799.258 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 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0DP23 | ||||||||
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#2: 化合物 | ChemComp-CA / #3: 化合物 | #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 | N | |
-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: 2.53 Å3/Da / 溶媒含有率: 51.37 % |
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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: 0.2 M Magnesium chloride hexahydrate, 0.1 M Tris pH 8.5, 20% w/v PEG 8000 |
-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: Australian Synchrotron / ビームライン: MX2 / 波長: 0.953736 Å |
検出器 | タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年11月28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: 0.953736 Å / 相対比: 1 |
反射 | 解像度: 1.85→38.87 Å / Num. obs: 14766 / % possible obs: 99.9 % / 冗長度: 13.4 % / Biso Wilson estimate: 21.3 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.6 |
反射 シェル | 解像度: 1.85→1.89 Å / Num. unique obs: 900 / CC1/2: 0.776 |
-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: 6EEB 解像度: 1.95→37.83 Å / SU ML: 0.1806 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 28.6328 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
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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 / 溶媒モデル: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 28.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.95→37.83 Å
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拘束条件 |
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LS精密化 シェル |
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