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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 1r5i | ||||||
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タイトル | Crystal structure of the MAM-MHC complex | ||||||
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![]() | IMMUNE SYSTEM / superantigen / MHC / MAM / complex | ||||||
機能・相同性 | ![]() regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / intermediate filament / transport vesicle membrane / polysaccharide binding / T-helper 1 type immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / T cell receptor binding / negative regulation of T cell proliferation / detection of bacterium / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / clathrin-dependent endocytosis of virus by host cell / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / lysosome / host cell surface receptor binding / immune response / positive regulation of protein phosphorylation / external side of plasma membrane / Golgi membrane / fusion of virus membrane with host plasma membrane / lysosomal membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / positive regulation of DNA-templated transcription / virion membrane / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() ![]() | ||||||
![]() | Zhao, Y. / Li, Z. / Drozd, S.J. / Guo, Y. / Mourad, W. / Li, H. | ||||||
![]() | ![]() タイトル: Crystal structure of Mycoplasma arthritidis mitogen complexed with HLA-DR1 reveals a novel superantigen fold and a dimerized superantigen-MHC complex. 著者: Zhao, Y. / Li, Z. / Drozd, S.J. / Guo, Y. / Mourad, W. / Li, H. | ||||||
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 | ![]() | 253 KB | 表示 | ![]() |
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PDB形式 | ![]() | 205.7 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 | ![]() 1dlhS 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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単位格子 |
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要素
-HLA class II histocompatibility antigen, ... , 2種, 4分子 AEBF
#1: タンパク質 | 分子量: 21225.512 Da / 分子数: 2 / 断片: alpha chain of class II MHC (residues 26-206) / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() #2: タンパク質 | 分子量: 22080.664 Da / 分子数: 2 / 断片: beta chain of class II MHC (residues 30-219) / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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-タンパク質・ペプチド / タンパク質 , 2種, 4分子 CGDH
#3: タンパク質・ペプチド | 分子量: 1506.807 Da / 分子数: 2 / 断片: haemagglutinin peptide (residues 306-318) / 由来タイプ: 合成 詳細: The peptide was chemically synthesized. This sequence occurs naturally in influenza virus. 参照: UniProt: P11133 #4: タンパク質 | 分子量: 25589.617 Da / 分子数: 2 / 由来タイプ: 組換発現 由来: (組換発現) ![]() プラスミド: pGEX-6P-1 / 生物種 (発現宿主): Escherichia coli / 発現宿主: ![]() ![]() |
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-非ポリマー , 2種, 110分子 ![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: 化合物 | ChemComp-PO4 / #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: 3.94 Å3/Da / 溶媒含有率: 68.78 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7.5 詳細: potassium sodium hosphate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 手法: 蒸気拡散法, ハンギングドロップ法 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: ![]() ![]() ![]() |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2003年6月8日 |
放射 | モノクロメーター: graphite / 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: 0.979 Å / 相対比: 1 |
反射 | 解像度: 2.6→43 Å / Num. all: 65311 / Num. obs: 65311 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 3.6 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 15 |
反射 シェル | 解像度: 2.6→2.7 Å / 冗長度: 3.1 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.489 / % possible all: 80.4 |
反射 | *PLUS % possible obs: 95.9 % / Rmerge(I) obs: 0.08 |
反射 シェル | *PLUS % possible obs: 80.4 % |
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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 1DLH 解像度: 2.6→42.23 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3119994.31 / Data cutoff low absF: 0 / 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: 29.9383 Å2 / ksol: 0.345188 e/Å3 | |||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 45.7 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: 2.6→42.23 Å
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拘束条件 |
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Refine LS restraints NCS | NCS model details: CONSTR | |||||||||||||||||||||||||
LS精密化 シェル | 解像度: 2.6→2.76 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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精密化 | *PLUS 最高解像度: 2.6 Å / 最低解像度: 100 Å | |||||||||||||||||||||||||
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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