+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7nhu | ||||||
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タイトル | Crystal structure of desB30 insulin produced by cell free protein synthesis | ||||||
要素 | (Insulin) x 2 | ||||||
キーワード | HORMONE / In vitro transcription/translation / insulin / zinc-free / dimer | ||||||
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 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / フーリエ合成 / 解像度: 1.4 Å | ||||||
データ登録者 | Johansson, E. | ||||||
引用 | ジャーナル: Protein Expr.Purif. / 年: 2021 タイトル: Cell free protein synthesis versus yeast expression - A comparison using insulin as a model protein. 著者: Jensen, A.B. / Hubalek, F. / Stidsen, C.E. / Johansson, E. / Oberg, F.K. / Skjot, M. / Kjeldsen, T. | ||||||
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 | 7nhu.cif.gz | 52.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7nhu.ent.gz | 32.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7nhu.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 | 7nhu_validation.pdf.gz | 301.8 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7nhu_full_validation.pdf.gz | 301.8 KB | 表示 | |
XML形式データ | 7nhu_validation.xml.gz | 4.8 KB | 表示 | |
CIF形式データ | 7nhu_validation.cif.gz | 6.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/nh/7nhu ftp://data.pdbj.org/pub/pdb/validation_reports/nh/7nhu | HTTPS FTP |
-関連構造データ
関連構造データ | 6s34S S: 精密化の開始モデル |
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類似構造データ |
-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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Components on special symmetry positions |
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-要素
#1: タンパク質・ペプチド | 分子量: 2383.698 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P01308 |
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#2: タンパク質・ペプチド | 分子量: 3332.849 Da / 分子数: 1 / Mutation: des30 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P01308 |
#3: 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 |
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-試料調製
結晶 | マシュー密度: 3.45 Å3/Da / 溶媒含有率: 64.36 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.2 M sodium formate, 20 % (w/v) PEG 3350 |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: 回転陽極 / タイプ: RIGAKU FR-X / 波長: 1.54184 Å |
検出器 | タイプ: DECTRIS EIGER X 1M / 検出器: PIXEL / 日付: 2020年8月6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: 1.54184 Å / 相対比: 1 |
反射 | 解像度: 1.4→38.97 Å / Num. obs: 15199 / % possible obs: 97.1 % / 冗長度: 28.9 % / Biso Wilson estimate: 20.99 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.06932 / Rpim(I) all: 0.01238 / Rrim(I) all: 0.07046 / Net I/σ(I): 53.42 |
反射 シェル | 解像度: 1.4→1.452 Å / 冗長度: 4.9 % / Rmerge(I) obs: 0.7383 / Num. unique obs: 5656 / CC1/2: 0.657 / CC star: 0.891 / Rpim(I) all: 0.3383 / Rrim(I) all: 0.8191 / % possible all: 72.72 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: フーリエ合成 開始モデル: 6S34 解像度: 1.4→38.97 Å / SU ML: 0.1484 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 25.925 立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 25.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.4→38.97 Å
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拘束条件 |
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LS精密化 シェル |
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精密化 TLS | 手法: refined / Origin x: -19.4319357786 Å / Origin y: -1.43200591852 Å / Origin z: -9.23223739059 Å
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精密化 TLSグループ | Selection details: all |