+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2omq | ||||||
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タイトル | VEALYL peptide derived from human insulin chain B, residues 12-17 | ||||||
要素 | VEALYL peptide derived from human insulin chain B, residues 12-17 | ||||||
キーワード | PROTEIN FIBRIL / steric zipper / anti-parallel beta-sheet | ||||||
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 | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2 Å | ||||||
データ登録者 | Ivanova, M. / Sawaya, M.R. / Eisenberg, D. | ||||||
引用 | ジャーナル: Nature / 年: 2007 タイトル: Atomic structures of amyloid cross-beta spines reveal varied steric zippers. 著者: Sawaya, M.R. / Sambashivan, S. / Nelson, R. / Ivanova, M.I. / Sievers, S.A. / Apostol, M.I. / Thompson, M.J. / Balbirnie, M. / Wiltzius, J.J. / McFarlane, H.T. / Madsen, A. / Riekel, C. / Eisenberg, 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 | 2omq.cif.gz | 12.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2omq.ent.gz | 8.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2omq.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/om/2omq ftp://data.pdbj.org/pub/pdb/validation_reports/om/2omq | 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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1 |
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単位格子 |
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詳細 | A steric zipper can be generated by repeated unit cell translations of the asymmetric unit along the b axis. |
-要素
#1: タンパク質・ペプチド | 分子量: 706.827 Da / 分子数: 4 / 断片: residues 12-17 / 由来タイプ: 合成 / 参照: UniProt: P01308*PLUS #2: 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: 1 |
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-試料調製
結晶化 | 温度: 310 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 2.5 詳細: 2mM peptide in 100 mM NaCl and 50 mM phosphate. Crystals can be more easily reproduced by dissolving peptide to 2 mM in water at room temperature, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K |
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-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: ESRF / ビームライン: ID13 / 波長: 0.9466 | ||||||||||||||||||||||||||||||||||||
検出器 | タイプ: MAR CCD 165 mm / 検出器: CCD / 日付: 2005年7月16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: 0.9466 Å / 相対比: 1 | ||||||||||||||||||||||||||||||||||||
反射 | 解像度: 1.7→90 Å / Num. obs: 820 / % possible obs: 93 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.172 / Χ2: 1.065 / Net I/σ(I): 3.9 | ||||||||||||||||||||||||||||||||||||
反射 シェル |
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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: polyalanine beta strands with ideal geometry 解像度: 2→21.84 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.375 / SU ML: 0.192 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.293 / 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: 18.338 Å2
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精密化ステップ | サイクル: LAST / 解像度: 2→21.84 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2→2.052 Å / Total num. of bins used: 20 /
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