+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6ck2 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Insulin analog containing a YB26W mutation | |||||||||
要素 |
| |||||||||
キーワード | HORMONE (ホルモン) / Long-acting / Basal / Therapeutic (治療) / Peptide Hormone (ペプチドホルモン) / Diabetes (糖尿病) / Biomolecular Engineering | |||||||||
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: 2.25 Å | |||||||||
データ登録者 | Rege, N.K. / Yee, V.C. / Weiss, M.A. | |||||||||
資金援助 | 米国, 2件
| |||||||||
引用 | ジャーナル: J. Biol. Chem. / 年: 2018 タイトル: Structure-based stabilization of insulin as a therapeutic protein assembly via enhanced aromatic-aromatic interactions. 著者: Rege, N.K. / Wickramasinghe, N.P. / Tustan, A.N. / Phillips, N.F.B. / Yee, V.C. / Ismail-Beigi, F. / Weiss, M.A. | |||||||||
履歴 |
|
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
---|
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6ck2.cif.gz | 35.9 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb6ck2.ent.gz | 23.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6ck2.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/ck/6ck2 ftp://data.pdbj.org/pub/pdb/validation_reports/ck/6ck2 | HTTPS FTP |
---|
-関連構造データ
関連構造データ | 4e7uS S: 精密化の開始モデル |
---|---|
類似構造データ |
-リンク
-集合体
登録構造単位 |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
単位格子 |
| ||||||||||||
Components on special symmetry positions |
|
-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: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P01308 #2: タンパク質・ペプチド | 分子量: 3441.955 Da / 分子数: 2 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P01308 |
---|
-非ポリマー , 4種, 44分子
#3: 化合物 | #4: 化合物 | ChemComp-IPH / | #5: 化合物 | ChemComp-CL / | #6: 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 |
---|
-試料調製
結晶 | マシュー密度: 1.98 Å3/Da / 溶媒含有率: 37.75 % |
---|---|
結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8 詳細: Crystals were obtained by hanging-drop vapor diffusion at room temperature in the presence of a 1:1.7 ratio of Zn2+ to protein monomer and a 3.5:1 ratio of phenol to protein monomer in Tris-HCl PH範囲: 7.8-9.0 |
-データ収集
回折 | 平均測定温度: 100 K |
---|---|
放射光源 | 由来: シンクロトロン / サイト: SSRL / ビームライン: BL7-1 / 波長: 0.9795 Å |
検出器 | タイプ: ADSC QUANTUM 315r / 検出器: CCD / 日付: 2016年5月12日 |
放射 | モノクロメーター: Side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg. 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: 2.25→33.04 Å / Num. obs: 4273 / % possible obs: 99.5 % / 冗長度: 10.1 % / Rmerge(I) obs: 0.03698 / Net I/σ(I): 45.78 |
反射 シェル | 解像度: 2.25→2.5755 Å / 冗長度: 9.6 % / Rmerge(I) obs: 0.1028 / Mean I/σ(I) obs: 8.99 / % possible all: 99.8 |
-解析
ソフトウェア |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: 分子置換 開始モデル: 4E7U 解像度: 2.25→33.031 Å / SU ML: 0.26 / 交差検証法: FREE R-VALUE / σ(F): 1.98 / 位相誤差: 26.74
| ||||||||||||||||||||||||||||
溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å | ||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.25→33.031 Å
| ||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||
LS精密化 シェル |
|