+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1ev6 | ||||||
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タイトル | Structure of the monoclinic form of the M-cresol/insulin R6 hexamer | ||||||
要素 | (INSULINインスリン) x 2 | ||||||
キーワード | HORMONE/GROWTH FACTOR / R6 Hexameric Insulin / HORMONE-GROWTH FACTOR COMPLEX | ||||||
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 / 解像度: 1.9 Å | ||||||
データ登録者 | Smith, G.D. / Ciszak, E. / Magrum, L.A. / Pangborn, W.A. / Blessing, R.H. | ||||||
引用 | ジャーナル: Biochem.Biophys.Res.Commun. / 年: 2000 タイトル: R6 Hexameric Insulin Complexed with m-Cresol or Resorcinol 著者: Smith, G.D. / Ciszak, E. / Magrum, L.A. / Pangborn, W.A. / Blessing, R.H. #1: ジャーナル: Nature / 年: 1989 タイトル: Phenol Stabilizes more Helix in a New Symmetrical Zinc Insulin Hexamer 著者: Derewenda, U. / Derewenda, Z. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D. / Smith, G.D. / Sparks, C. / Swenson, D. #2: ジャーナル: Proteins / 年: 1992 タイトル: Structure of a Rhombohedral R6 Insulin/Phenol Complex 著者: Smith, G.D. / Dodson, G.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 | 1ev6.cif.gz | 74.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1ev6.ent.gz | 61.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1ev6.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/ev/1ev6 ftp://data.pdbj.org/pub/pdb/validation_reports/ev/1ev6 | 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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-要素
-タンパク質・ペプチド , 2種, 12分子 ACEGIKBDFHJL
#1: タンパク質・ペプチド | 分子量: 2383.698 Da / 分子数: 6 / 断片: RESIDUES 87-107 / 由来タイプ: 合成 詳細: This sequence occurs naturally in homo sapiens (human) 参照: UniProt: P01308 #2: タンパク質・ペプチド | 分子量: 3433.953 Da / 分子数: 6 / 断片: RESIDUES 25-54 / 由来タイプ: 合成 詳細: This sequence occurs naturally in homo sapiens (human) 参照: UniProt: P01308 |
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-非ポリマー , 5種, 242分子
#3: 化合物 | ChemComp-CRS / #4: 化合物 | #5: 化合物 | #6: 化合物 | ChemComp-NA / | #7: 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 | マシュー密度: 2.4 Å3/Da / 溶媒含有率: 48.64 % | ||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 298 K / 手法: slow cooling / pH: 6.5 詳細: 30 mg insulin, 3.0 ml 0.02 M HCl, 0.3 ml 0.15 M Zinc Acetate, 1.5 ml 0.2 M Sodium Citrate, 1.2 ml 5% m-Cresol in ethanol, pH 6.5, SLOW COOLING, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 手法: unknown | ||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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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: 回転陽極 / タイプ: RIGAKU RU200 / 波長: 1.54178 |
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 2000年1月18日 / 詳細: OSMIC CONFOCAL MIRRORS |
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: 1.54178 Å / 相対比: 1 |
反射 | 解像度: 1.8→20.95 Å / Num. all: 28441 / Num. obs: 28441 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 6.15 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 40.6 |
反射 シェル | 解像度: 1.89→1.94 Å / 冗長度: 2.2 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 5.4 / % possible all: 92.6 |
反射 | *PLUS Num. measured all: 174925 |
反射 シェル | *PLUS % possible obs: 92.6 % |
-解析
ソフトウェア |
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精密化 | 解像度: 1.9→20.95 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: restrained / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: Engh & Huber
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 45.11 Å2 / ksol: 0.292 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 33.7 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 1.9→20.95 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.9→2.02 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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ソフトウェア | *PLUS 名称: CNS / バージョン: 1 / 分類: refinement | ||||||||||||||||||||||||||||||||||||
精密化 | *PLUS σ(F): 0 / % reflection Rfree: 9.9 % | ||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 33.7 Å2 | ||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.333 / % reflection Rfree: 9.5 % / Rfactor Rwork: 0.271 / Rfactor obs: 0.271 |