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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: 4fka | ||||||
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タイトル | High resolution structure of the manganese derivative of insulin | ||||||
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![]() | HORMONE / manganese-insulin derivative | ||||||
機能・相同性 | ![]() negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of respiratory burst / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / negative regulation of acute inflammatory response / alpha-beta T cell activation / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / negative regulation of lipid catabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / positive regulation of glycolytic process / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / Regulation of insulin secretion / endosome lumen / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin-like growth factor receptor binding / wound healing / insulin receptor binding / regulation of synaptic plasticity / negative regulation of protein catabolic process / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / regulation of protein localization / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / positive regulation of NF-kappaB transcription factor activity / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / secretory granule lumen / protease binding / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / G protein-coupled receptor signaling pathway / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / extracellular space / extracellular region / identical protein binding 類似検索 - 分子機能 | ||||||
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手法 | ![]() ![]() ![]() | ||||||
![]() | Prugovecki, B. / Pulic, I. / Toth, M. / Matkovic-Calogovic, D. | ||||||
![]() | ![]() タイトル: High Resolution Structure of the Manganese Derivative of Insulin 著者: Prugovecki, B. / Pulic, I. / Toth, M. / Matkovic-Calogovic, D. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 62.8 KB | 表示 | ![]() |
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-検証レポート
文書・要旨 | ![]() | 454.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 456.4 KB | 表示 | |
XML形式データ | ![]() | 10.1 KB | 表示 | |
CIF形式データ | ![]() | 13.7 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 3exxS 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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Components on special symmetry positions |
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要素
#1: タンパク質・ペプチド | 分子量: 2383.698 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) ![]() #2: タンパク質・ペプチド | 分子量: 3433.953 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) ![]() #3: 化合物 | ChemComp-NA / | #4: 化合物 | #5: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 1.86 Å3/Da / 溶媒含有率: 33.94 % |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.4 詳細: The protein solution consisted of 7.5 mg mL-1 of zinc-free insulin in 0.02 mol L-1 hydrochloric acid. The reservoir solution was at pH 6.4 containing 1mM sodium citrate, volume fraction of ...詳細: The protein solution consisted of 7.5 mg mL-1 of zinc-free insulin in 0.02 mol L-1 hydrochloric acid. The reservoir solution was at pH 6.4 containing 1mM sodium citrate, volume fraction of aceton 10 % ,9 mmol L-1 manganese(II) sulphate monohydrate and redistilled water, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-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: ![]() ![]() ![]() |
検出器 | タイプ: MARRESEARCH / 検出器: CCD |
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 Å / 相対比: 1 |
反射 | 解像度: 1→10.48 Å / Num. obs: 43875 / % possible obs: 96.7 % / 冗長度: 2.7 % / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 11 |
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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: ![]() 開始モデル: pdb entry 3EXX 解像度: 1.08→10.28 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 0.753 / SU ML: 0.018 / 交差検証法: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.038 / 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: 8.583 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.08→10.28 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.08→1.108 Å / Total num. of bins used: 20
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