+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2vjz | ||||||
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タイトル | Crystal structure form ultalente insulin microcrystals | ||||||
要素 |
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キーワード | HORMONE (ホルモン) / CARBOHYDRATE METABOLISM (炭水化物代謝) / GLUCOSE METABOLISM (炭水化物代謝) / MICRO FOCUS BEAMLINE / INSULIN (インスリン) / SECRETED (分泌) / MICRO CRYSTAL / CLEAVAGE ON PAIR OF BASIC RESIDUES / DISEASE MUTATION / DIABETES MELLITUS (糖尿病) | ||||||
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: 1.8 Å | ||||||
データ登録者 | Wagner, A. / Diez, J. / Schulze-Briese, C. / Schluckebier, G. | ||||||
引用 | ジャーナル: Proteins / 年: 2009 タイトル: Crystal Structure of Ultralente-A Microcrystalline Insulin Suspension. 著者: Wagner, A. / Diez, J. / Schulze-Briese, C. / Schluckebier, G. | ||||||
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 | 2vjz.cif.gz | 37.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2vjz.ent.gz | 26.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2vjz.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/vj/2vjz ftp://data.pdbj.org/pub/pdb/validation_reports/vj/2vjz | 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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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 / 断片: RESIDUES 90-110 / 由来タイプ: 組換発現 詳細: PRECURSOR CRYSTALS ULTRALENTE INSULIN CRYSTALS PROCESS 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P01308 #2: タンパク質・ペプチド | 分子量: 3433.953 Da / 分子数: 2 / 断片: RESIDUES 25-54 / 由来タイプ: 組換発現 / 詳細: PRECURSOR CRYSTALS FROM THE ULTRALENTE PROCESS / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: SACCHAROMYCES CEREVISIAE (パン酵母) / 参照: UniProt: P01308 #3: 化合物 | #4: 化合物 | ChemComp-CL / #5: 水 | ChemComp-HOH / | |
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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: 3 |
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-試料調製
結晶 | マシュー密度: 1.77 Å3/Da / 溶媒含有率: 37 % / 解説: NONE |
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結晶化 | pH: 7.5 / 詳細: pH 7.5 |
-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: SLS / ビームライン: X06SA / 波長: 0.9183 |
検出器 | タイプ: MARRESEARCH / 検出器: CCD / 詳細: MICRO FOCUS |
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: 0.9183 Å / 相対比: 1 |
反射 | 解像度: 1.8→32.4 Å / Num. obs: 33133 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / 冗長度: 4.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.5 |
反射 シェル | 解像度: 1.8→1.9 Å / 冗長度: 2.3 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.8 / % possible all: 84.4 |
-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: PDB ENTRY 1TRZ 解像度: 1.8→32.43 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.558 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.155 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STURCTURE DETERMINATION FROM MICROCRYSTALS 8 X8 X 3 MICRO METER
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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: 31.64 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.8→32.43 Å
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拘束条件 |
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