+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1jk8 | ||||||
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タイトル | Crystal structure of a human insulin peptide-HLA-DQ8 complex | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / HLA-DQ8 / insulin B peptide / type 1 diabetes (1型糖尿病) / autoimmunity (自己免疫) | ||||||
機能・相同性 | 機能・相同性情報 : / MHC class II receptor activity / transport vesicle membrane / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / Insulin processing ...: / MHC class II receptor activity / transport vesicle membrane / negative regulation of NAD(P)H oxidase activity / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / Signaling by Insulin receptor / IRS activation / nitric oxide-cGMP-mediated signaling / Insulin processing / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / regulation of protein secretion / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of peptide hormone secretion / plasma membrane => GO:0005886 / positive regulation of respiratory burst / Regulation of gene expression in beta cells / 液性免疫 / negative regulation of acute inflammatory response / alpha-beta T cell activation / Generation of second messenger molecules / negative regulation of respiratory burst involved in inflammatory response / PD-1 signaling / positive regulation of dendritic spine maintenance / Synthesis, secretion, and deacylation of Ghrelin / positive regulation of glycogen biosynthetic process / negative regulation of protein secretion / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of gluconeogenesis / positive regulation of nitric oxide mediated signal transduction / fatty acid homeostasis / regulation of protein localization to plasma membrane / COPI-mediated anterograde transport / negative regulation of lipid catabolic process / type II interferon-mediated signaling pathway / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / positive regulation of insulin receptor signaling pathway / negative regulation of reactive oxygen species biosynthetic process / 小胞 / positive regulation of protein autophosphorylation / Insulin receptor recycling / insulin-like growth factor receptor binding / MHC class II antigen presentation / NPAS4 regulates expression of target genes / positive regulation of protein metabolic process / neuron projection maintenance / positive regulation of brown fat cell differentiation / endoplasmic reticulum-Golgi intermediate compartment membrane / activation of protein kinase B activity / positive regulation of glycolytic process / Insulin receptor signalling cascade / positive regulation of mitotic nuclear division / trans-Golgi network membrane / Regulation of insulin secretion / positive regulation of long-term synaptic potentiation / endosome lumen / positive regulation of cytokine production / acute-phase response / positive regulation of protein secretion / lumenal side of endoplasmic reticulum membrane / positive regulation of nitric-oxide synthase activity / regulation of transmembrane transporter activity / positive regulation of cell differentiation / positive regulation of glucose import / negative regulation of proteolysis / regulation of synaptic plasticity / clathrin-coated endocytic vesicle membrane / wound healing / insulin receptor binding / ER to Golgi transport vesicle membrane / hormone activity / negative regulation of protein catabolic process / 認識 / positive regulation of neuron projection development / peptide antigen assembly with MHC class II protein complex / Golgi lumen / MHC class II protein complex / positive regulation of protein localization to nucleus / vasodilation / peptide antigen binding / glucose metabolic process / endocytic vesicle membrane / regulation of protein localization / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / glucose homeostasis / Downstream TCR signaling / cell-cell signaling / insulin receptor signaling pathway / MHC class II protein complex binding / late endosome membrane / positive regulation of NF-kappaB transcription factor activity / T cell receptor signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.4 Å | ||||||
データ登録者 | Lee, K.H. / Wucherpfennig, K.W. / Wiley, D.C. | ||||||
引用 | ジャーナル: Nat.Immunol. / 年: 2001 タイトル: Structure of a human insulin peptide-HLA-DQ8 complex and susceptibility to type 1 diabetes. 著者: Lee, K.H. / Wucherpfennig, K.W. / Wiley, D.C. | ||||||
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 | 1jk8.cif.gz | 88.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1jk8.ent.gz | 69.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1jk8.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/jk/1jk8 ftp://data.pdbj.org/pub/pdb/validation_reports/jk/1jk8 | HTTPS FTP |
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-関連構造データ
-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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-要素
#1: タンパク質 | 分子量: 20734.102 Da / 分子数: 1 / 断片: alpha chain (DQA1*0301) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P04225, UniProt: P01909*PLUS |
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#2: タンパク質 | 分子量: 22333.100 Da / 分子数: 1 / 断片: beta chain (DQB1*0302) / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 発現宿主: Spodoptera frugiperda (ツマジロクサヨトウ) 参照: UniProt: P01920 |
#3: タンパク質・ペプチド | 分子量: 1479.721 Da / 分子数: 1 / 断片: peptide (9-SHLVEALYLVCGERG-23) / 由来タイプ: 合成 詳細: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN HUMANS (HOMO SAPIENS). 参照: GenBank: 3776078, UniProt: P01308*PLUS |
#4: 糖 | ChemComp-NAG / |
#5: 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: 2.71 Å3/Da / 溶媒含有率: 54.64 % | |||||||||||||||||||||||||
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 3.5 詳細: PEG 8000, magnesium acetate, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 18K | |||||||||||||||||||||||||
結晶化 | *PLUS | |||||||||||||||||||||||||
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: APS / ビームライン: 14-BM-C / 波長: 1 Å |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2000年1月1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 Å / 相対比: 1 |
反射 | 解像度: 2.4→30 Å / Num. obs: 18183 / % possible obs: 95 % / Biso Wilson estimate: 10.9 Å2 / Rmerge(I) obs: 0.103 |
反射 | *PLUS 最低解像度: 30 Å / % possible obs: 95 % |
反射 シェル | *PLUS 最高解像度: 2.4 Å / 最低解像度: 2.49 Å / Rmerge(I) obs: 0.362 |
-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 / 解像度: 2.4→29.16 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1016975.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 2
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 24.6514 Å2 / ksol: 0.335285 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 23 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: 2.4→29.16 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.4→2.55 Å / Rfactor Rfree error: 0.021 / 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): 2 / % reflection Rfree: 9.9 % | ||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS 最低解像度: 2.42 Å / Rfactor Rfree: 0.311 / % reflection Rfree: 9.7 % / Rfactor Rwork: 0.315 |