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基本情報
登録情報 | データベース: PDB / ID: 1xw7 | ||||||
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タイトル | Diabetes-Associated Mutations in Human Insulin: Crystal Structure and Photo-Cross-Linking Studies of A-Chain Variant Insulin Wakayama | ||||||
![]() | (Insulin) x 2 | ||||||
![]() | HORMONE/GROWTH FACTOR / Leu-A30insulin / protein unfolding / insulin receptor / HORMONE-GROWTH FACTOR COMPLEX | ||||||
機能・相同性 | ![]() 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 / 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 / negative regulation of protein catabolic process / hormone activity / cognition / positive regulation of neuron projection development / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / glucose metabolic process / regulation of protein localization / insulin receptor signaling pathway / cell-cell signaling / glucose homeostasis / positive regulation of NF-kappaB transcription factor activity / 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 | ||||||
手法 | ![]() ![]() | ||||||
![]() | Wan, Z.L. / Huang, K. / Xu, B. / Chu, Y.C. / Hu, S.Q. / Katsoyannis, P.G. / Weiss, M.A. | ||||||
![]() | ![]() タイトル: Diabetes-associated mutations in human insulin: crystal structure and photo-cross-linking studies of a-chain variant insulin wakayama 著者: Wan, Z.L. / Huang, K. / Xu, B. / Hu, S.Q. / Wang, S. / Chu, Y.C. / Katsoyannis, P.G. / Weiss, M.A. #1: ![]() タイトル: Crystallographic titration of cubic insulin crystals: pH affects GluB13 switching and sulfate binding 著者: Diao, J. #2: ジャーナル: Biophys.J. / 年: 1998 タイトル: Structure of cubic insulin crystals in glucose solutions 著者: Yu, B. / Caspar, D.L. #3: ジャーナル: Acta Crystallogr.,Sect.B / 年: 1991 タイトル: Structure of the pig insulin dimer in the cubic crystal 著者: Badger, J. / Harris, M.R. / Reynolds, C.D. / Evans, A.C. / Dodson, E.J. / Dodson, G.G. / North, A.C. #4: ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 1991 タイトル: Water structure in cubic insulin crystals 著者: Badager, J. / Caspar, D.L. #5: ジャーナル: J.Mol.Biol. / 年: 1978 タイトル: Zinc-free cubic pig insulin: crystallization and structure determination 著者: Dodson, E.J. / Dodson, G.G. / Lewitova, A. / Sabesan, M. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 36.4 KB | 表示 | ![]() |
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PDB形式 | ![]() | 24.9 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-関連構造データ
関連構造データ | ![]() 1zegS S: 精密化の開始モデル |
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類似構造データ |
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リンク
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集合体
登録構造単位 | ![]()
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4 | ![]()
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単位格子 |
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Components on special symmetry positions |
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詳細 | The biological assembly is a hexamer generated from the dimer in the asymmetric unit by the operations |
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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: 2397.725 Da / 分子数: 2 / 変異: V3L / 由来タイプ: 合成 詳細: The peptide was chemically synthesized. The sequence of the peptide is naturally found 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 / 由来タイプ: 合成 詳細: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human). 参照: UniProt: P01308 |
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-非ポリマー , 4種, 86分子 ![](data/chem/img/IPH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#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: ![]() |
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試料調製
結晶 | マシュー密度: 2.54 Å3/Da / 溶媒含有率: 51.6 % |
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結晶化 | 温度: 290 K / pH: 6.2 詳細: Tris, sodium citrate, acetone, phenol, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 290K, pH 6.20 |
-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: ![]() |
検出器 | タイプ: BRUKER / 検出器: CCD / 日付: 2004年7月23日 |
放射 | モノクロメーター: 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: 1.54 Å / 相対比: 1 |
反射 | 解像度: 2.3→50.1 Å / Num. obs: 5346 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / 冗長度: 12.9 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.7 |
反射 シェル | 解像度: 2.3→2.44 Å / 冗長度: 9.8 % / Rmerge(I) obs: 0.066 / Mean I/σ(I) obs: 9.6 / % possible all: 95.2 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: PDB ENTRY 1ZEG 解像度: 2.3→50.1 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 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: 71.24 Å2 / ksol: 0.38 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 46.9 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: 2.3→50.1 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.3→2.44 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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