+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5hpr | ||||||
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タイトル | Insulin with proline analog HyP at position B28 in the T2 state | ||||||
要素 |
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キーワード | HORMONE (ホルモン) / Insulin (インスリン) / non-canonical amino acid / hydroxyproline (ヒドロキシプロリン) / non-natural amino acid / unnatural amino acid (タンパク質を構成しないアミノ酸) | ||||||
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: 1.33 Å | ||||||
データ登録者 | Lieblich, S.A. / Fang, K.Y. / Cahn, J.K.B. / Tirrell, D.A. | ||||||
資金援助 | デンマーク, 1件
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引用 | ジャーナル: J. Am. Chem. Soc. / 年: 2017 タイトル: 4S-Hydroxylation of Insulin at ProB28 Accelerates Hexamer Dissociation and Delays Fibrillation. 著者: Lieblich, S.A. / Fang, K.Y. / Cahn, J.K.B. / Rawson, J. / LeBon, J. / Ku, H.T. / Tirrell, D.A. | ||||||
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 | 5hpr.cif.gz | 39.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5hpr.ent.gz | 26.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5hpr.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/hp/5hpr ftp://data.pdbj.org/pub/pdb/validation_reports/hp/5hpr | HTTPS FTP |
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-関連構造データ
-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・ペプチド | 分子量: 2383.698 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: INS / プラスミド: pQE80L / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): CAG18515 / 参照: UniProt: P01308 |
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#2: タンパク質・ペプチド | 分子量: 3449.953 Da / 分子数: 1 / Mutation: Pro28Hyp / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: INS / プラスミド: pQE80L / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): CAG18515 / 参照: UniProt: P01308 |
#3: 化合物 | ChemComp-NA / |
#4: 化合物 | ChemComp-GOL / |
#5: 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: 3.42 Å3/Da / 溶媒含有率: 64.05 % |
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結晶化 | 温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8 詳細: 300 mM Tris, 0.5 mM zinc acetate, 8.5% acetone, 0.5 M sodium citrate |
-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: シンクロトロン / サイト: SSRL / ビームライン: BL12-2 / 波長: 0.9795 Å | ||||||||||||||||||
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2015年6月24日 | ||||||||||||||||||
放射 | モノクロメーター: LIQUID NITROGEN-COOLED DOUBLE CRYSTAL K-B FOCUSING MIRRORS 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: 0.9795 Å / 相対比: 1 | ||||||||||||||||||
反射 | 解像度: 1.33→55.33 Å / Num. obs: 18244 / % possible obs: 99.4 % / 冗長度: 5.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.4 | ||||||||||||||||||
反射 シェル |
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-位相決定
位相決定 | 手法: 分子置換 |
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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: 分子置換 開始モデル: 3T2A 解像度: 1.33→55.33 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.041 / SU ML: 0.02 / 交差検証法: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.037 / 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: 19.801 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.33→55.33 Å
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拘束条件 |
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