+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1g7a | ||||||
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タイトル | 1.2 A structure of T3R3 human insulin at 100 K | ||||||
要素 |
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キーワード | hormone/growth factor / T3R3 Insulin Hexamer / 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 / シンクロトロン / 分子置換 / 解像度: 1.2 Å | ||||||
データ登録者 | Smith, G.D. / Pangborn, W.A. / Blessing, R.H. | ||||||
引用 | ジャーナル: Acta Crystallogr.,Sect.D / 年: 2001 タイトル: Phase changes in T(3)R(3)(f) human insulin: temperature or pressure induced? 著者: Smith, G.D. / Pangborn, W.A. / Blessing, R.H. #1: ジャーナル: Biochemistry / 年: 1995 タイトル: X-ray Crystallographic Studies on Hexameric Insulins in the Presence of Helix-Stabilizing Agents, Thiocyanate, Methylparaben, and Phenol 著者: Whittingham, J.L. / Chaudhuri, S. / Dodson, E.J. / Moody, P.C.E. / Dodson, G.G. #2: ジャーナル: Biochemistry / 年: 1994 タイトル: Crystallographic Evidence for Dual Coordination around Zinc in the T3R3 Human Insulin Hexamer 著者: Ciszak, E. / Smith, G.D. #3: ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 1984 タイトル: Structural stability in the 4-zinc human insulin hexamer 著者: Smith, G.D. / Swenson, D.C. / Dodson, E.J. / Dodson, G.G. / Reynolds, C.D. #4: ジャーナル: Nature / 年: 1976 タイトル: Structure of 4-zinc insulin 著者: Bentley, G. / Dodson, E. / Dodson, G.G. / Hodgkin, D. / Mercola, D. #5: ジャーナル: Acta Crystallogr.,Sect.D / 年: 2000 タイトル: The First Protein Crystal Structure Determined from High Resolution X-Ray Powder Diffraction Data: A Variant of T3R3 Human Insulin Zinc Complex Produced by Grinding 著者: Von Dreele, R.B. / Stephens, P.W. / Smith, G.D. / Blessing, R.H. | ||||||
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 | 1g7a.cif.gz | 100.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1g7a.ent.gz | 79.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1g7a.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 | 1g7a_validation.pdf.gz | 493.1 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1g7a_full_validation.pdf.gz | 497.3 KB | 表示 | |
XML形式データ | 1g7a_validation.xml.gz | 14.9 KB | 表示 | |
CIF形式データ | 1g7a_validation.cif.gz | 21.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/g7/1g7a ftp://data.pdbj.org/pub/pdb/validation_reports/g7/1g7a | 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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詳細 | The second dimer of the T3R3 insulin hexamer is generated by the crystallographic three-fold axis: -y, x-y, z / The third dimer of the T3R3 insulin hexamer is generated by the crystallographic three-fold axis: y-x, -x, z |
-要素
-タンパク質・ペプチド , 2種, 8分子 ACEGBDFH
#1: タンパク質・ペプチド | 分子量: 2383.698 Da / 分子数: 4 / 断片: A-CHAIN / 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: 4 / 断片: B-CHAIN / 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, 292分子
#3: 化合物 | ChemComp-ZN / #4: 化合物 | ChemComp-CL / #5: 化合物 | #6: 化合物 | ChemComp-GOL / | #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: 1.9 Å3/Da / 溶媒含有率: 35.26 % | ||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 298 K / 手法: slow cooling / pH: 6.3 詳細: 5 mg/ml human insulin, 0.01 M HCl, 0.007 M zinc acetate, 0.05 M sodium citrate, 17% acetone, 1.0 M NaCl. pH 6.3, SLOW COOLING at 298K | ||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 手法: microgravity | ||||||||||||||||||||||||||||||||||||||||||
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: シンクロトロン / サイト: NSLS / ビームライン: X8C / 波長: 0.8 Å |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 1999年3月20日 |
放射 | モノクロメーター: Silicon / 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: 0.8 Å / 相対比: 1 |
反射 | 解像度: 1.2→31.2 Å / Num. all: 53646 / Num. obs: 53646 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 8.6 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 42.8 |
反射 シェル | 解像度: 1.2→1.23 Å / 冗長度: 5.3 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 7.1 / Num. unique all: 3598 / % possible all: 100 |
反射 | *PLUS % possible obs: 100 % / Num. measured all: 925256 |
反射 シェル | *PLUS % possible obs: 75.9 % |
-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 1trz 解像度: 1.2→31.2 Å / Rfactor Rfree error: 0.003 / 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: 73.9 Å2 / ksol: 0.44 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 17 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: 1.2→31.2 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.2→1.28 Å / Rfactor Rfree error: 0.009 / 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 最高解像度: 1.2 Å / 最低解像度: 31.2 Å / σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.169 | ||||||||||||||||||||||||||||||||||||
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 Rfree: 0.259 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.24 |