+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2vll | ||||||
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タイトル | The Structural Dynamics and Energetics of an Immunodominant T-cell Receptor are Programmed by its Vbeta Domain | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / GLYCOPROTEIN (糖タンパク質) / TRANSMEMBRANE (膜貫通型タンパク質) / UBL CONJUGATION / IMMUNE SYSTEM-RECEPTOR-COMPLEX (免疫系) / IMMUNOGLOBULIN DOMAIN (免疫グロブリンフォールド) / HOST-VIRUS INTERACTION / PYRROLIDONE CARBOXYLIC ACID (ピログルタミン酸) / IMMUNE RESPONSE (免疫応答) / IMMUNODOMINANCE / DISEASE MUTATION / MEMBRANE (生体膜) / SECRETED (分泌) / RECEPTOR (受容体) / GLYCATION (糖化反応) / POLYMORPHISM / TCR / FLU / MHC / MHC I / T-CELL (T細胞) / COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / 出芽 / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery ...Assembly of Viral Components at the Budding Site / Influenza Infection / Fusion of the Influenza Virion to the Host Cell Endosome / Release / 出芽 / Packaging of Eight RNA Segments / Uncoating of the Influenza Virion / Entry of Influenza Virion into Host Cell via Endocytosis / Viral RNP Complexes in the Host Cell Nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / endoplasmic reticulum exit site / Viral mRNA Translation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / detection of bacterium / T cell receptor binding / viral budding from plasma membrane / 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 / 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 / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / 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 / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / positive regulation of type II interferon production / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / E3 ubiquitin ligases ubiquitinate target proteins / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / structural constituent of virion / learning or memory / defense response to Gram-positive bacterium / 免疫応答 / Amyloid fiber formation / lysosomal membrane 類似検索 - 分子機能 | ||||||
生物種 | HOMO SAPIENS (ヒト) UNIDENTIFIED INFLUENZA VIRUS (インフルエンザウイルス) | ||||||
手法 | X線回折 / シンクロトロン / 多波長異常分散 / 解像度: 1.6 Å | ||||||
データ登録者 | Ishizuka, J. / Stewart-Jones, G. / Van Der Merwe, A. / Bell, J. / Mcmichael, A. / Jones, Y. | ||||||
引用 | ジャーナル: Immunity / 年: 2008 タイトル: The Structural Dynamics and Energetics of an Immunodominant T-Cell Receptor are Programmed by its Vbeta Domain 著者: Ishizuka, J. / Stewart-Jones, G. / Van Der Merwe, A. / Bell, J. / Mcmichael, A. / Jones, Y. | ||||||
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. |
-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 | 2vll.cif.gz | 190.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2vll.ent.gz | 155.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2vll.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/vl/2vll ftp://data.pdbj.org/pub/pdb/validation_reports/vl/2vll | 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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単位格子 |
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-要素
#1: タンパク質 | 分子量: 31951.316 Da / 分子数: 2 / 断片: HLA-A2, RESIDUES 25-300 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P01892, UniProt: P04439*PLUS #2: タンパク質 | 分子量: 11879.356 Da / 分子数: 2 / 断片: RESIDUES 21-119 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P61769 #3: タンパク質・ペプチド | 分子量: 966.174 Da / 分子数: 2 / 由来タイプ: 合成 由来: (合成) UNIDENTIFIED INFLUENZA VIRUS (インフルエンザウイルス) 参照: UniProt: P03485*PLUS #4: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: X線回折 |
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-試料調製
結晶 | マシュー密度: 2.3 Å3/Da / 溶媒含有率: 49.5 % / 解説: NONE |
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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: ESRF / ビームライン: ID14-2 / 波長: 0.933 |
検出器 | タイプ: ADSC CCD / 検出器: CCD |
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: 0.933 Å / 相対比: 1 |
反射 | 解像度: 1.6→3 Å / Num. obs: 100261 / % possible obs: 89.7 % / Observed criterion σ(I): 1.9 / 冗長度: 6.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22 |
反射 シェル | 解像度: 1.6→1.64 Å / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.9 / % possible all: 62.4 |
-解析
ソフトウェア | 名称: REFMAC / バージョン: 5.2.0005 / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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精密化 | 構造決定の手法: 多波長異常分散 開始モデル: NONE 解像度: 1.6→72.17 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.986 / SU ML: 0.072 / 交差検証法: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.114 / 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: 1.2 Å / 溶媒モデル: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 23.51 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.6→72.17 Å
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拘束条件 |
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