+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5e7w | ||||||
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タイトル | X-ray Structure of Human Recombinant 2Zn insulin at 0.92 Angstrom | ||||||
要素 | (Insulinインスリン) x 2 | ||||||
キーワード | IMMUNE SYSTEM (免疫系) / Insulin (インスリン) / human (ヒト) / recombinant / high-resolution (解像度) | ||||||
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 / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / 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: 0.9519 Å | ||||||
データ登録者 | Lisgarten, D.R. / Naylor, C.E. / Palmer, R.A. / Lobley, C.M.C. | ||||||
引用 | ジャーナル: Chem Cent J / 年: 2017 タイトル: Ultra-high resolution X-ray structures of two forms of human recombinant insulin at 100 K. 著者: Lisgarten, D.R. / Palmer, R.A. / Lobley, C.M.C. / Naylor, C.E. / Chowdhry, B.Z. / Al-Kurdi, Z.I. / Badwan, A.A. / Howlin, B.J. / Gibbons, N.C.J. / Saldanha, J.W. / Lisgarten, J.N. / Basak, A.K. | ||||||
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 | 5e7w.cif.gz | 87.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5e7w.ent.gz | 67.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5e7w.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/e7/5e7w ftp://data.pdbj.org/pub/pdb/validation_reports/e7/5e7w | HTTPS FTP |
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-関連構造データ
関連構造データ | 3w7yS 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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単位格子 |
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Components on special symmetry positions |
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-要素
-タンパク質・ペプチド , 2種, 4分子 ACBD
#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: 組換発現 詳細: Human Insulin A and C Chain Insulin was purchased from Insugen 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: INS / 発現宿主: Komagataella pastoris (菌類) / 参照: UniProt: P01308 #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: 組換発現 詳細: Human Insulin B and D chain Insulin was purchased from Insugen 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: INS / 発現宿主: Komagataella pastoris (菌類) / 参照: UniProt: P01308 |
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-非ポリマー , 4種, 224分子
#3: 化合物 | #4: 化合物 | ChemComp-ACT / | #5: 化合物 | ChemComp-POL / | #6: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: X線回折 |
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-試料調製
結晶 | マシュー密度: 1.89 Å3/Da / 溶媒含有率: 35 % / 解説: needle |
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結晶化 | 温度: 293 K / 手法: batch mode / pH: 6.3 詳細: The crystals were prepared by a batch method similar to that of Baker et al, 1988 [1], modified as follows: 0.01g of insulin as a fine powder was placed in a clean test tube; 0.02M HCl was ...詳細: The crystals were prepared by a batch method similar to that of Baker et al, 1988 [1], modified as follows: 0.01g of insulin as a fine powder was placed in a clean test tube; 0.02M HCl was added to dissolve the protein; on addition of 0.15 mL of 0.15 M zinc acetate the solution became cloudy due to precipitation of the protein; 0.3 mL of acetone and then 0.5 mL of trisodium citrate together with 0.8 mL of water were added and the solution went clear; the pH was checked and increased with NaOH to a pH between 8 and 9 for different batches, thus ensuring complete dissolution. It was then adjusted to the required value of pH 6.3. If any slight turbidity occurred, it was removed by warming the solution. The solution was then filtered using a Millipore membrane/acetate cellulose acetate filter. This removes any nuclei which will encourage precipitation or formation of masses of small crystals. The solution was then warmed to 50 deg C by surrounding the test tube with preheated water in a Dewar. This allowed the solution to cool slowly to room temperature. The test tube was lightly sealed with cling film; crystals formed within a few days and were of suitable size for X-ray diffraction within two weeks; the test tube containing crystals was kept at 4 degC prior to data collection. The crystal used for data collection was about 0.2 mm3. PH範囲: 6.2 - 6.4 / Temp details: Room Temperature |
-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: Diamond / ビームライン: I02 / 波長: 0.77 Å |
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2012年9月27日 詳細: Data were collected at 16000keV (0.77 Angstrom) and 100 deg K with the Pilatus 6M detector as close to the sample as possible (179.5mm). The EDNA strategy was used to obtain a start angle and ...詳細: Data were collected at 16000keV (0.77 Angstrom) and 100 deg K with the Pilatus 6M detector as close to the sample as possible (179.5mm). The EDNA strategy was used to obtain a start angle and 180 deg of data were collected with 0.1 deg oscillation and 0.1s exposure. The resolution of useful diffraction data achieved and used for structure analysis was 0.92 Angstrom. |
放射 | モノクロメーター: Beamline fixed at 16000keV / 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: 0.77 Å / 相対比: 1 |
反射 | 解像度: 0.92→40.91 Å / Num. obs: 58647 / % possible obs: 100 % / 冗長度: 5 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 20.2 |
反射 シェル | 解像度: 0.92→0.94 Å / 冗長度: 4.7 % / Rmerge(I) obs: 0.967 / Mean I/σ(I) obs: 1.6 / % 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: 3W7Y 解像度: 0.9519→10 Å / 交差検証法: FREE R-VALUE / σ(F): 0
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原子変位パラメータ | Biso mean: 18.45 Å2 | ||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 0.9519→10 Å
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