+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1ev3 | ||||||
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タイトル | Structure of the rhombohedral form of the M-cresol/insulin R6 hexamer | ||||||
要素 | (INSULIN) x 2 | ||||||
キーワード | HORMONE/GROWTH FACTOR / R6 Hexamer / 18-A / 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 / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion ...negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / alpha-beta T cell activation / regulation of cellular amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / Signal attenuation / negative regulation of lipid catabolic process / negative regulation of gluconeogenesis / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / negative regulation of reactive oxygen species biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / neuron projection maintenance / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / activation of protein kinase B activity / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of glycolytic process / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / positive regulation of nitric-oxide synthase activity / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / acute-phase response / Regulation of insulin secretion / negative regulation of protein catabolic process / endosome lumen / positive regulation of glucose import / positive regulation of protein secretion / negative regulation of proteolysis / positive regulation of cell differentiation / regulation of transmembrane transporter activity / insulin receptor binding / wound healing / regulation of synaptic plasticity / vasodilation / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / glucose metabolic process / regulation of protein localization / glucose homeostasis / insulin receptor signaling pathway / cell-cell signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of NF-kappaB transcription factor activity / positive regulation of cell growth / protease binding / secretory granule lumen / 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 / Golgi membrane / endoplasmic reticulum lumen / 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: 1.78 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: Acta Crystallogr.,Sect.D / 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: Proteins / 年: 1992 タイトル: Structure of a Rhombohedral R6 Insulin/Phenol Complex 著者: Smith, G.D. / Dodson, G.G. #2: 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. | ||||||
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 | 1ev3.cif.gz | 30.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1ev3.ent.gz | 24.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1ev3.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
文書・要旨 | 1ev3_validation.pdf.gz | 450.6 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1ev3_full_validation.pdf.gz | 451.7 KB | 表示 | |
XML形式データ | 1ev3_validation.xml.gz | 7.6 KB | 表示 | |
CIF形式データ | 1ev3_validation.cif.gz | 9.6 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ev/1ev3 ftp://data.pdbj.org/pub/pdb/validation_reports/ev/1ev3 | HTTPS FTP |
-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
-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 / 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: 2 / 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 , 4種, 95分子
#3: 化合物 | #4: 化合物 | #5: 化合物 | #6: 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: 2.03 Å3/Da / 溶媒含有率: 39.41 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 298 K / 手法: slow cooling / pH: 8.5 詳細: 30 mg insulin, 3.0 ml of 0.02 M HCl, 0.3 ml of 0.15 M Zinc Acetate, 1.5 ml of 0.2 M Sodium Citrate, 1.2 ml of 2.5% m-cresol in acetone, 0.36 gm sodium chloride, pH 8.5, SLOW COOLING, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
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13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: 1.7→19.72 Å / Num. all: 9334 / Num. obs: 9334 / % possible obs: 92.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 6.9 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 60.6 |
反射 シェル | 解像度: 1.78→1.83 Å / 冗長度: 3 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 10 / % possible all: 82.6 |
反射 | *PLUS Num. measured all: 64359 |
反射 シェル | *PLUS % possible obs: 82.6 % |
-解析
ソフトウェア |
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精密化 | 解像度: 1.78→19.72 Å / Rfactor Rfree error: 0.009 / 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: 56.69 Å2 / ksol: 0.342 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 33.2 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: 1.78→19.72 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.78→1.89 Å / Rfactor Rfree error: 0.32 / 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: 10.3 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 33.2 Å2 | ||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.371 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.336 / Rfactor obs: 0.336 |