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基本情報
登録情報 | データベース: PDB / ID: 1ogt | |||||||||
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タイトル | CRYSTAL STRUCTURE OF HLA-B*2705 COMPLEXED WITH THE VASOACTIVE INTESTINAL PEPTIDE TYPE 1 RECEPTOR (VIPR) PEPTIDE (RESIDUES 400-408) | |||||||||
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![]() | IMMUNE SYSTEM / IMMUNE SYSTEM-COMPLEX / MHC (MAJOR HISTOCOMPATIBILITY COMPLEX) / HLA- B*2705 | |||||||||
機能・相同性 | ![]() antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / : / : / vasoactive intestinal polypeptide receptor activity / : / neutrophil degranulation / regulation of membrane depolarization / G protein-coupled peptide receptor activity / regulation of interleukin-12 production ...antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / : / : / vasoactive intestinal polypeptide receptor activity / : / neutrophil degranulation / regulation of membrane depolarization / G protein-coupled peptide receptor activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / antigen processing and presentation of peptide antigen via MHC class I / retina homeostasis / regulation of T cell anergy / regulation of interleukin-6 production / type I interferon-mediated signaling pathway / plasma membrane => GO:0005886 / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / TAP binding / protection from natural killer cell mediated cytotoxicity / regulation of immune response / type II interferon-mediated signaling pathway / detection of bacterium / viral process / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / defense response / negative regulation of neurogenesis / Glucagon-type ligand receptors / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / G alpha (s) signalling events / cellular response to lipopolysaccharide / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | ![]() ![]() ![]() | |||||||||
![]() | Hulsmeyer, M. / Fiorillo, M.T. / Bettosini, F. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. | |||||||||
![]() | ![]() タイトル: Dual, HLA-B27 subtype-dependent conformation of a self-peptide. 著者: Hulsmeyer, M. / Fiorillo, M.T. / Bettosini, F. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. #1: ![]() タイトル: Hla-B27 Subtypes Differentially Associated with Disease Exhibit Subtle Structural Alterations 著者: Hulsmeyer, M. / Hillig, R.C. / Volz, A. / Ruhl, M. / Schroder, W. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. #2: ![]() タイトル: The Three-Dimensional Structure of Hla-B27 at 2.1 A Resolution Suggests a General Mechanism for Tight Peptide Binding to Mhc 著者: Madden, D.R. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C. | |||||||||
履歴 |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
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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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PDBx/mmCIF形式 | ![]() | 217.8 KB | 表示 | ![]() |
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PDB形式 | ![]() | 173.5 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
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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
-タンパク質 , 2種, 2分子 AB
#1: タンパク質 | 分子量: 31928.160 Da / 分子数: 1 / 断片: EXTRACELLULAR DOMAIN, RESIDUES 25-300 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
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#2: タンパク質 | 分子量: 11879.356 Da / 分子数: 1 / 断片: RESIDUES 21-119 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() |
-タンパク質・ペプチド , 1種, 1分子 C
#3: タンパク質・ペプチド | 分子量: 1399.694 Da / 分子数: 1 / 断片: RESIDUES 400-408 / 由来タイプ: 合成 / 詳細: THIS PEPTIDE WAS CHEMICALLY SYNTHESISED / 由来: (合成) ![]() |
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-非ポリマー , 3種, 727分子 ![](data/chem/img/GOL.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/HOH.gif)
#4: 化合物 | ChemComp-GOL / #5: 化合物 | ChemComp-MN / | #6: 水 | ChemComp-HOH / | |
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-詳細
構成要素の詳細 | B*2705:INVOLVED IN THE PRESENTATION OF FOREIGN ANTIGENS TO THE IMMUNE SYSTEM. B*2075 MOLECULES ...B*2705:INVOLVED IN THE PRESENTATI |
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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: 2.9 Å3/Da / 溶媒含有率: 56.9 % | ||||||||||||||||||||||||||||||||||||||||||
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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: 8 詳細: TRIS PH 8.0, 16% PEG 8000, HANGING DROP, TEMPERATURE 291K | ||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS pH: 7.5 / 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: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 2002年11月25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: 0.898 Å / 相対比: 1 |
反射 | 解像度: 1.47→50 Å / Num. obs: 84476 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / 冗長度: 4.2 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.3 |
反射 シェル | 解像度: 1.47→1.53 Å / 冗長度: 3.3 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.2 / % possible all: 95.2 |
反射 | *PLUS 最高解像度: 1.47 Å / 最低解像度: 50 Å / 冗長度: 4.2 % / Rmerge(I) obs: 0.078 |
反射 シェル | *PLUS % possible obs: 95.2 % / 冗長度: 3.3 % / Num. unique obs: 8185 / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 2.2 |
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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 1OF2 解像度: 1.47→62.02 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.017 / SU ML: 0.038 / 交差検証法: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.061 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.4 Å / 溶媒モデル: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 17.28 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.47→62.02 Å
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拘束条件 |
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