+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8pi5 | ||||||
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タイトル | Crystal structure of human insulin desB30 precursor with an Alanine-Methionine-Lysine C-peptide in hexamer (T3R3) conformation | ||||||
要素 | Insulin B chain,Insulin A chain | ||||||
キーワード | HORMONE / insulin / precursor / dimer | ||||||
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 / 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 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 1.66 Å | ||||||
データ登録者 | Johansson, E. / Schluckebier, G. | ||||||
資金援助 | デンマーク, 1件
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引用 | ジャーナル: Trends Biotechnol / 年: 2024 タイトル: Molecular engineering of insulin for recombinant expression in yeast. 著者: Kjeldsen, T. / Andersen, A.S. / Hubalek, F. / Johansson, E. / Kreiner, F.F. / Schluckebier, G. / Kurtzhals, P. | ||||||
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 | 8pi5.cif.gz | 81 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8pi5.ent.gz | 58.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8pi5.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
文書・要旨 | 8pi5_validation.pdf.gz | 440.6 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8pi5_full_validation.pdf.gz | 441 KB | 表示 | |
XML形式データ | 8pi5_validation.xml.gz | 7.5 KB | 表示 | |
CIF形式データ | 8pi5_validation.cif.gz | 9.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/pi/8pi5 ftp://data.pdbj.org/pub/pdb/validation_reports/pi/8pi5 | HTTPS FTP |
-関連構造データ
-リンク
-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 | 分子量: 6029.985 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: INS / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P01308 #2: 化合物 | ChemComp-ZN / #3: 化合物 | ChemComp-CL / | #4: 化合物 | ChemComp-RCO / | #5: 水 | ChemComp-HOH / | 研究の焦点であるリガンドがあるか | N | |
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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: 1.97 Å3/Da / 溶媒含有率: 37.52 % |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 9 詳細: 6 mg/ml protein, 20 mM resorcinol, 0.5 Zn2+ (from zinc acetate) per insuln monomer in water, pH 7.95 precipitant: 0.1 M Bicine, pH 9.0, 2 % (v/v) 1,4-dioxane, 10 % (w/v) PEG 20000 |
-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: 回転陽極 / タイプ: RIGAKU MICROMAX-007 HF / 波長: 1.542 Å |
検出器 | タイプ: MAR scanner 345 mm plate / 検出器: IMAGE PLATE / 日付: 2013年1月22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: 1.542 Å / 相対比: 1 |
反射 | 解像度: 1.66→13.66 Å / Num. obs: 10563 / % possible obs: 97.17 % / 冗長度: 6.1 % / Biso Wilson estimate: 21.26 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.04731 / Rpim(I) all: 0.01975 / Rrim(I) all: 0.05135 / Net I/σ(I): 25.54 |
反射 シェル | 解像度: 1.66→1.72 Å / 冗長度: 2.5 % / Rmerge(I) obs: 0.3121 / Mean I/σ(I) obs: 3.58 / Num. unique obs: 829 / CC1/2: 0.847 / CC star: 0.958 / Rpim(I) all: 0.2031 / Rrim(I) all: 0.375 / % possible all: 76.19 |
-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 / 解像度: 1.66→13.66 Å / SU ML: 0.1539 / 交差検証法: FREE R-VALUE / σ(F): 1.96 / 位相誤差: 22.8241 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: 29.36 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.66→13.66 Å
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拘束条件 |
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LS精密化 シェル |
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