+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3o7l | ||||||
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タイトル | Crystal Structure of phospholamban (1-19):PKA C-subunit:AMP-PNP:Mg2+ complex | ||||||
要素 |
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キーワード | TRANSFERASE (転移酵素) / Protein Kinase A (プロテインキナーゼA) / Phospholamban / Allostery (アロステリック効果) / Substrate Recognition / Conformational Selection / Intrinsically Disordered Proteins (天然変性タンパク質) / Membrane Proteins (膜タンパク質) | ||||||
機能・相同性 | 機能・相同性情報 negative regulation of calcium ion binding / negative regulation of calcium ion import into sarcoplasmic reticulum / negative regulation of ATPase-coupled calcium transmembrane transporter activity / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / regulation of relaxation of muscle / Ion transport by P-type ATPases / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling ...negative regulation of calcium ion binding / negative regulation of calcium ion import into sarcoplasmic reticulum / negative regulation of ATPase-coupled calcium transmembrane transporter activity / adenylate cyclase-activating adrenergic receptor signaling pathway involved in heart process / regulation of relaxation of muscle / Ion transport by P-type ATPases / regulation of the force of heart contraction by cardiac conduction / calcium ion-transporting ATPase complex / spontaneous exocytosis of neurotransmitter / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / negative regulation of meiotic cell cycle / HDL assembly / DARPP-32 events / Rap1 signalling / PKA activation / Vasopressin regulates renal water homeostasis via Aquaporins / Regulation of insulin secretion / GPER1 signaling / Hedgehog 'off' state / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / regulation of calcium ion import / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / MAPK6/MAPK4 signaling / GLI3 is processed to GLI3R by the proteasome / AURKA Activation by TPX2 / negative regulation of heart contraction / Factors involved in megakaryocyte development and platelet production / Regulation of PLK1 Activity at G2/M Transition / Interleukin-3, Interleukin-5 and GM-CSF signaling / CD209 (DC-SIGN) signaling / ATPase inhibitor activity / RET signaling / regulation of the force of heart contraction / negative regulation of ATP-dependent activity / Ion homeostasis / regulation of cardiac muscle cell contraction / VEGFA-VEGFR2 Pathway / cardiac muscle tissue development / nucleotide-activated protein kinase complex / regulation of cellular respiration / regulation of protein processing / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / regulation of heart contraction / プロテインキナーゼA / cellular response to cold / sperm capacitation / regulation of osteoblast differentiation / cAMP-dependent protein kinase activity / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / negative regulation of heart rate / postsynaptic modulation of chemical synaptic transmission / response to zinc ion / response to testosterone / cellular response to glucagon stimulus / protein kinase A regulatory subunit binding / axoneme / plasma membrane raft / calcium channel regulator activity / regulation of calcium ion transport / mesoderm formation / sperm flagellum / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / negative regulation of smoothened signaling pathway / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / regulation of proteasomal protein catabolic process / protein kinase A signaling / positive regulation of gluconeogenesis / Notchシグナリング / regulation of ryanodine-sensitive calcium-release channel activity / regulation of synaptic transmission, glutamatergic / negative regulation of TORC1 signaling / sperm midpiece / sarcoplasmic reticulum membrane / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / positive regulation of protein export from nucleus / 筋小胞体 / neural tube closure / cellular response to glucose stimulus / ミトコンドリア / modulation of chemical synaptic transmission / response to insulin / neuromuscular junction / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / 転写後修飾 / small GTPase binding / intracellular calcium ion homeostasis / calcium ion transport 類似検索 - 分子機能 | ||||||
生物種 | Mus musculus (ハツカネズミ) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.8 Å | ||||||
データ登録者 | Cheng, C.Y. / Taylor, S.S. | ||||||
引用 | ジャーナル: Nat.Chem.Biol. / 年: 2010 タイトル: Dynamics connect substrate recognition to catalysis in protein kinase A. 著者: Masterson, L.R. / Cheng, C. / Yu, T. / Tonelli, M. / Kornev, A. / Taylor, S.S. / Veglia, 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 | 3o7l.cif.gz | 275.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3o7l.ent.gz | 219.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3o7l.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/o7/3o7l ftp://data.pdbj.org/pub/pdb/validation_reports/o7/3o7l | HTTPS FTP |
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-関連構造データ
関連構造データ | 1atpS S: 精密化の開始モデル |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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-要素
-CAMP-dependent protein kinase catalytic subunit ... , 2種, 2分子 BD
#1: タンパク質 | 分子量: 40577.340 Da / 分子数: 1 / 断片: phospholamban peptide / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Pkaca, Prkaca / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P05132, プロテインキナーゼA |
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#2: タンパク質 | 分子量: 40657.316 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Pkaca, Prkaca / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P05132, プロテインキナーゼA |
-タンパク質・ペプチド , 1種, 1分子 I
#3: タンパク質・ペプチド | 分子量: 1738.022 Da / 分子数: 1 / 由来タイプ: 合成 詳細: Chemically synthesized. This sequence occurs naturally from Phospholamban 参照: UniProt: P61014 |
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-非ポリマー , 4種, 25分子
#4: 化合物 | #5: 化合物 | ChemComp-PEG / | #6: 化合物 | ChemComp-ANP / | #7: 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: 2.84 Å3/Da / 溶媒含有率: 56.71 % |
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: The complex was obtained by combining a 1:10:10:10 molar ratio mixture of PKA-C (7 mg/ml), PLN1-19, MgCl2, and AMP-PNP in 20 mM sodium acetate (pH 6.5), 180 mM KCl, and 5 mM DTT, VAPOR ...詳細: The complex was obtained by combining a 1:10:10:10 molar ratio mixture of PKA-C (7 mg/ml), PLN1-19, MgCl2, and AMP-PNP in 20 mM sodium acetate (pH 6.5), 180 mM KCl, and 5 mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-データ収集
回折 | 平均測定温度: 200 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: 8.2.2 / 波長: 1 Å |
検出器 | タイプ: ADSC QUANTUM 315 / 検出器: CCD / 日付: 2009年1月1日 |
放射 | モノクロメーター: GRAPHITE / 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: 2.8→50 Å / Num. obs: 26095 / % possible obs: 99.5 % / Observed criterion σ(F): 264629 / Observed criterion σ(I): 264629 / 冗長度: 10.5 % / Biso Wilson estimate: 51.6 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.063 / Net I/σ(I): 38.8 |
反射 シェル | 解像度: 2.8→2.88 Å / Mean I/σ(I) obs: 5.1 / % possible all: 100 |
-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: PDB ENTRY 1ATP 解像度: 2.8→39.086 Å / SU ML: 0.45 / Isotropic thermal model: Isotropic / 交差検証法: THROUGHOUT / σ(F): 1.34 / 立体化学のターゲット値: ML
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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 / Bsol: 39.117 Å2 / ksol: 0.288 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ |
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精密化ステップ | サイクル: LAST / 解像度: 2.8→39.086 Å
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拘束条件 |
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LS精密化 シェル |
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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