+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3mre | ||||||
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タイトル | Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288 nonapeptide | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / MHC class I (MHCクラスI分子) / HLA / IMMUNE RESPONSE (免疫応答) / NONAPEPTIDE (ペプチド) / VIRAL PEPTIDE / EPSTEIN-BARR VIRUS (エプスタイン・バール・ウイルス) / BMLF1 PROTEIN / EB2 protein | ||||||
機能・相同性 | 機能・相同性情報 symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / 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 ...symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / 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 / 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 / mRNA transport / beta-2-microglobulin binding / detection of bacterium / T cell receptor binding / 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 / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / 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 / Modulation by Mtb of host immune system / positive regulation of type II interferon production / 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 differentiation in thymus / T cell receptor signaling pathway / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / antibacterial humoral response / protein homotetramerization / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / learning or memory / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / defense response to Gram-positive bacterium / 免疫応答 / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / virus-mediated perturbation of host defense response / 小胞体 / ゴルジ体 / signaling receptor binding / focal adhesion / 自然免疫系 / host cell nucleus 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Epstein-Barr virus EBV (ヘルペスウイルス) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.1 Å | ||||||
データ登録者 | Gras, S. / Echasserieau, K. / Saulquin, X. / Bonneville, M. / Housset, D. | ||||||
引用 | ジャーナル: J.Immunol. / 年: 2014 タイトル: Analysis of Relationships between Peptide/MHC Structural Features and Naive T Cell Frequency in Humans. 著者: Reiser, J.B. / Legoux, F. / Gras, S. / Trudel, E. / Chouquet, A. / Leger, A. / Le Gorrec, M. / Machillot, P. / Bonneville, M. / Saulquin, X. / Housset, D. | ||||||
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 | 3mre.cif.gz | 121 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3mre.ent.gz | 92.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3mre.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/mr/3mre ftp://data.pdbj.org/pub/pdb/validation_reports/mr/3mre | 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: 34008.711 Da / 分子数: 1 / 断片: HLA-A*0201 alpha chain, UNP resiude 25-300 / 変異: A245V / 由来タイプ: 組換発現 詳細: C-terminal biotin acceptor peptide sequence tag (GSLHHILDAQKMVWNHR) 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA, HLA-A, HLAA / プラスミド: pHN1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): X90F LAQQ1 / 参照: UniProt: P01892 |
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#2: タンパク質 | 分子量: 11879.356 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: B2M, BETA-2 MICROGLUBULIN, CDABP0092, HDCMA22P / プラスミド: pHN1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): X90F LAQQ1 / 参照: UniProt: P61769 |
#3: タンパク質・ペプチド | 分子量: 920.191 Da / 分子数: 1 断片: EB2 PROTEIN FRAGMENT (BMLF1 280-288), UNP residues 300-308 由来タイプ: 合成 / 詳細: chemical synthesis 由来: (合成) Epstein-Barr virus EBV (ヘルペスウイルス) 参照: UniProt: Q3KSU1 |
#4: 水 | ChemComp-HOH / |
構成要素の詳細 | EBV BSFL2 AND BMLF1 ORFS ARE JOINED TO ENCODE THE EB2 PROTEIN. EB2 PROTEIN IS ALSO CALLED ...EBV BSFL2 AND BMLF1 ORFS ARE JOINED TO ENCODE THE EB2 PROTEIN. EB2 PROTEIN IS ALSO CALLED BSFL2/BMLF1, MTA OR SM. |
配列の詳細 | THE GLCTLVAML NONAPEPTIDE WAS FIRST IDENTIFIED AS AN HLA-A2 RESTRICTED T CELL EPITOPE ON A ...THE GLCTLVAML NONAPEPTID |
-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: 2.25 Å3/Da / 溶媒含有率: 45.32 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: 15% PEG 6000, 0.1M NaCitrate, 0.1M NaCl, 5mg/ml protein conc., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-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: ID14-3 / 波長: 0.931 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: MAR CCD 165 mm / 検出器: CCD / 日付: 2005年12月16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: 0.931 Å / 相対比: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 1.1→50 Å / Num. obs: 150866 / % possible obs: 90 % / Observed criterion σ(I): -3 / 冗長度: 3.72 % / Biso Wilson estimate: 12.358 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル | Diffraction-ID: 1
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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: 分子置換 開始モデル: PDB ENTRY 3GSO 解像度: 1.1→15 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0 / SU B: 0.551 / SU ML: 0.026 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R Free: 0.045 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: U VALUES: REFINED INDIVIDUALLY; 10 to 20 refinement cycles with all observed reflections were performed at the end of the refinement procedure, in order to obtain the most accurate model. ...詳細: U VALUES: REFINED INDIVIDUALLY; 10 to 20 refinement cycles with all observed reflections were performed at the end of the refinement procedure, in order to obtain the most accurate model. Rwork and Rfree values corresponds to the coordinates just before these very last cycles.
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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 max: 53.59 Å2 / Biso mean: 12.51 Å2 / Biso min: 2.65 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.1→15 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.1→1.128 Å / Total num. of bins used: 20
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