+
データを開く
-
基本情報
登録情報 | データベース: PDB / ID: 1jk8 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Crystal structure of a human insulin peptide-HLA-DQ8 complex | |||||||||
![]() |
| |||||||||
![]() | IMMUNE SYSTEM / HLA-DQ8 / insulin B peptide / type 1 diabetes / autoimmunity | |||||||||
機能・相同性 | ![]() MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of feeding behavior / transport vesicle membrane / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / IRS activation / Insulin processing ...MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of feeding behavior / transport vesicle membrane / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / humoral immune response / alpha-beta T cell activation / Generation of second messenger molecules / positive regulation of dendritic spine maintenance / Co-inhibition by PD-1 / Synthesis, secretion, and deacylation of Ghrelin / negative regulation of respiratory burst involved in inflammatory response / negative regulation of protein secretion / activation of protein kinase B activity / negative regulation of gluconeogenesis / positive regulation of insulin receptor signaling pathway / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / regulation of protein localization to plasma membrane / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / transport vesicle / nitric oxide-cGMP-mediated signaling / COPI-mediated anterograde transport / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / negative regulation of reactive oxygen species biosynthetic process / insulin-like growth factor receptor binding / positive regulation of brown fat cell differentiation / NPAS4 regulates expression of target genes / endoplasmic reticulum-Golgi intermediate compartment membrane / neuron projection maintenance / positive regulation of mitotic nuclear division / MHC class II antigen presentation / Insulin receptor signalling cascade / positive regulation of glycolytic process / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / trans-Golgi network membrane / endosome lumen / acute-phase response / lumenal side of endoplasmic reticulum membrane / positive regulation of protein secretion / positive regulation of D-glucose import / insulin receptor binding / positive regulation of cell differentiation / Regulation of insulin secretion / peptide antigen assembly with MHC class II protein complex / wound healing / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / negative regulation of protein catabolic process / positive regulation of neuron projection development / hormone activity / antigen processing and presentation of exogenous peptide antigen via MHC class II / regulation of synaptic plasticity / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / positive regulation of protein localization to nucleus / Golgi lumen / vasodilation / cognition / endocytic vesicle membrane / glucose metabolic process / Interferon gamma signaling / MHC class II protein complex binding / Downstream TCR signaling / late endosome membrane / insulin receptor signaling pathway / glucose homeostasis / cell-cell signaling / T cell receptor signaling pathway / regulation of protein localization / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / protease binding / secretory granule lumen / adaptive immune response / endosome membrane / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / immune response 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | ![]() ![]() ![]() | |||||||||
![]() | Lee, K.H. / Wucherpfennig, K.W. / Wiley, D.C. | |||||||||
資金援助 | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
構造の表示
構造ビューア | 分子: ![]() ![]() |
---|
-
ダウンロードとリンク
-
ダウンロード
PDBx/mmCIF形式 | ![]() | 96.6 KB | 表示 | ![]() |
---|---|---|---|---|
PDB形式 | ![]() | 69.9 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 466.2 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 477 KB | 表示 | |
XML形式データ | ![]() | 19.9 KB | 表示 | |
CIF形式データ | ![]() | 25.9 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
リンク
-
集合体
登録構造単位 | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
単位格子 |
|
-
要素
#1: タンパク質 | 分子量: 20690.092 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) ![]() 発現宿主: ![]() ![]() 参照: UniProt: Q5Y7H0, UniProt: P01909*PLUS |
---|---|
#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) ![]() 発現宿主: ![]() ![]() 参照: UniProt: O19714, UniProt: P01920*PLUS |
#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). 由来: (合成) ![]() |
#4: 糖 | ChemComp-NAG / |
#5: 水 | ChemComp-HOH / |
研究の焦点であるリガンドがあるか | N |
Has protein modification | Y |
-実験情報
-実験
実験 | 手法: ![]() |
---|
-
試料調製
結晶 | マシュー密度: 2.71 Å3/Da / 溶媒含有率: 54.64 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
---|---|
放射光源 | 由来: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 24.65 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 23 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.4→29.16 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 |