+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1os4 | ||||||
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タイトル | Dehydrated T6 human insulin at 295 K | ||||||
要素 | (Insulin) x 2 | ||||||
キーワード | HORMONE/GROWTH FACTOR / Air dried crystal / data measured at 298 K / 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 amino acid metabolic process / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / Synthesis, secretion, and deacylation of Ghrelin / regulation of protein localization to plasma membrane / fatty acid homeostasis / negative regulation of gluconeogenesis / negative regulation of lipid catabolic process / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / COPI-mediated anterograde transport / positive regulation of lipid biosynthetic process / positive regulation of insulin receptor signaling pathway / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / nitric oxide-cGMP-mediated signaling / positive regulation of protein autophosphorylation / insulin-like growth factor receptor binding / transport vesicle / Insulin receptor recycling / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of protein metabolic process / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / positive regulation of nitric-oxide synthase activity / acute-phase response / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / cognition / Regulation of insulin secretion / endosome lumen / positive regulation of D-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 / negative regulation of protein catabolic process / regulation of synaptic plasticity / hormone activity / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / cell-cell signaling / insulin receptor signaling pathway / positive regulation of NF-kappaB transcription factor activity / glucose homeostasis / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / 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 / endoplasmic reticulum lumen / Golgi membrane / negative regulation of gene expression / positive regulation of cell population proliferation / regulation of DNA-templated transcription / positive regulation of gene expression / 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 / 分子置換 / 解像度: 2.25 Å | ||||||
データ登録者 | Smith, G.D. / Blessing, R.H. | ||||||
引用 | ジャーナル: Acta Crystallogr.,Sect.D / 年: 2003 タイトル: Lessons from an aged, dried crystal of T(6) human insulin. 著者: Smith, G.D. / Blessing, R.H. #1: ジャーナル: Acta Crystallogr.,Sect.D / 年: 2003 タイトル: The structure of T6 human insulin at 1.0 A resolution. 著者: Smith, G.D. / Pangborn, W.A. / Blessing, R.H. #2: ジャーナル: Philos.Trans.R.Soc.London,Ser.B / 年: 1988 タイトル: The structure of 2Zn pig insulin crystals at 1.5 A resoltuion. 著者: Baker, E.N. / Blundel, T.L. / Cutfield, J.F. / Cutfield, S.M. / Dodson, E.J. / Dodson, G.G. / Hodgkin, D.M.C. / Hubbard, R.E. / Isaacs, N.W. / Reynolds, C.D. #3: ジャーナル: Acta Crystallogr.,Sect.B / 年: 1989 タイトル: Structure of insulin: Results of joint neutron and X-ray refinement. 著者: Wlodawer, A. / Savage, H. / Dodson, 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 | 1os4.cif.gz | 67.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1os4.ent.gz | 51.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1os4.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 | 1os4_validation.pdf.gz | 514.9 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1os4_full_validation.pdf.gz | 522.5 KB | 表示 | |
XML形式データ | 1os4_validation.xml.gz | 12.9 KB | 表示 | |
CIF形式データ | 1os4_validation.cif.gz | 17.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/os/1os4 ftp://data.pdbj.org/pub/pdb/validation_reports/os/1os4 | 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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詳細 | The biological assembly is a hexamer which is contained in the asymmetric unit. |
-要素
#1: タンパク質・ペプチド | 分子量: 2383.698 Da / 分子数: 6 / 断片: A-chain / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 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: B-chain / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P01308 #3: 化合物 | #4: 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: 2.12 Å3/Da / 溶媒含有率: 41.43 % | ||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 295 K / 手法: slow cooling / pH: 6.3 詳細: hydrochloric acid, zinc acetate, sodium citrate, acetone, pH 6.3, SLOW COOLING, temperature 295.K | ||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 手法: batch method | ||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 295 K |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU / 波長: 1.5418 Å |
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE / 日付: 2002年6月24日 / 詳細: mirrors |
放射 | モノクロメーター: Osmic confocal mirrors / 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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 2.25→41.64 Å / Num. all: 15512 / Num. obs: 10252 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 1.5 % / Biso Wilson estimate: 42.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.3 |
反射 シェル | 解像度: 2.25→2.33 Å / Rmerge(I) obs: 0.289 / Mean I/σ(I) obs: 1.6 / % possible all: 85.9 |
反射 | *PLUS % possible obs: 82.7 % / Num. measured all: 15512 / Rmerge(I) obs: 0.07 |
反射 シェル | *PLUS % possible obs: 85.9 % |
-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 4INS 解像度: 2.25→41.64 Å / Isotropic thermal model: Isotropic / 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: 65.3 Å2 / ksol: 0.41 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 44.8 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: 2.25→41.64 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.25→2.39 Å / Rfactor Rfree error: 0.029
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精密化 | *PLUS 最低解像度: 41.7 Å | ||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rwork: 0.31 |