+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6ves | |||||||||
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タイトル | Human insulin analog: [GluB10,HisA8,ArgA9]-DOI | |||||||||
要素 |
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キーワード | HORMONE (ホルモン) | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / 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 / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / negative regulation of fatty acid metabolic process / Insulin processing / negative regulation of feeding behavior / regulation of protein secretion / positive regulation of peptide hormone secretion / Regulation of gene expression in beta cells / positive regulation of respiratory burst / positive regulation of dendritic spine maintenance / alpha-beta T cell activation / negative regulation of acute inflammatory response / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / fatty acid homeostasis / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / positive regulation of lipid biosynthetic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / 小胞 / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / Regulation of insulin secretion / positive regulation of nitric-oxide synthase activity / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / wound healing / insulin receptor binding / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / 認識 / Golgi lumen / vasodilation / positive regulation of protein localization to nucleus / glucose metabolic process / regulation of protein localization / glucose homeostasis / cell-cell signaling / insulin receptor signaling pathway / 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 / 小胞体 / ゴルジ体 / 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 | |||||||||
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: 1.85 Å | |||||||||
データ登録者 | Menting, J.G. / Chou, D.H.-C. / Lawrence, M.C. / Xiong, X. | |||||||||
資金援助 | オーストラリア, 米国, 2件
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引用 | ジャーナル: To Be Published タイトル: Mini-Ins: A Minimal, Bioactive Insulin Analog with Alternative Binding Modes 著者: Xiong, X. / Menting, J. / Disotaur, M. / Agrawal, R. / Delaine, C. / MacRaild, C. / Ghabash, G. / Kim, J.H. / Olivera, B. / Safavi, H. / Norton, R. / Forbes, B. / Fisher, S. / Lawrence, M.C. / Chou, D. | |||||||||
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 | 6ves.cif.gz | 38.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6ves.ent.gz | 26.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6ves.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/ve/6ves ftp://data.pdbj.org/pub/pdb/validation_reports/ve/6ves | HTTPS FTP |
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-関連構造データ
関連構造データ | 4ogaS 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
#1: タンパク質・ペプチド | 分子量: 2490.857 Da / 分子数: 1 / 変異: T8H, S9R / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P01308 |
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#2: タンパク質・ペプチド | 分子量: 2481.845 Da / 分子数: 1 / 変異: H10E / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P01308 |
#3: 水 | ChemComp-HOH / |
-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: 1.85 Å3/Da / 溶媒含有率: 33.57 % |
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結晶化 | 温度: 300 K / 手法: 蒸気拡散法, シッティングドロップ法 詳細: WELL CONDITION: 0.2 M calcium acetate, 0.1 M imidazole (pH 8) + 10% w/v PEG 8000 Protein was provided as a sample comprising 5 mg/ml (IR310.T).Fv83-7 in 10mM HEPES-NaOH (pH7.5) + 0.02% NaN3 ...詳細: WELL CONDITION: 0.2 M calcium acetate, 0.1 M imidazole (pH 8) + 10% w/v PEG 8000 Protein was provided as a sample comprising 5 mg/ml (IR310.T).Fv83-7 in 10mM HEPES-NaOH (pH7.5) + 0.02% NaN3 plus three mol equivalents of the IR-A alphaCT peptide 704-719 plus 1.8 mol of the analog |
-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: 0.95373 Å |
検出器 | タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2017年8月2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: 0.95373 Å / 相対比: 1 |
反射 | 解像度: 1.85→46.94 Å / Num. obs: 3456 / % possible obs: 100 % / 冗長度: 6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.147 / Rpim(I) all: 0.066 / Rrim(I) all: 0.162 / Net I/σ(I): 7.4 |
反射 シェル | 解像度: 1.85→1.91 Å / 冗長度: 6.2 % / Rmerge(I) obs: 2.365 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 290 / CC1/2: 0.405 / Rpim(I) all: 1.014 / Rrim(I) all: 2.588 / % 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: Editted version of human insulin component of PDB entry 4OGA 解像度: 1.85→24.667 Å / SU ML: 0.19 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 26.43
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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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.85→24.667 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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