+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3bo8 | ||||||
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タイトル | The High Resolution Crystal Structure of HLA-A1 Complexed with the MAGE-A1 Peptide | ||||||
要素 |
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キーワード | IMMUNE SYSTEM / Melanoma Associated Antigen / MAGE / MAGE-A1 / Major Histocompatibility Complex / MHC / Human Leukocyte Antigen / HLA / HLA-A1 / HLA-A010101 / TCR / T-cell receptor / Antibody / Fab-Hyb3 / Hyb3 / Glycoprotein / Host-virus interaction / Immune response / Immunoglobulin domain / Membrane / MHC I / Sulfation / Transmembrane / Disease mutation / Glycation / Pyrrolidone carboxylic acid / Secreted / Tumor antigen | ||||||
機能・相同性 | 機能・相同性情報 T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / negative regulation of Notch signaling pathway / antigen processing and presentation of exogenous peptide antigen via MHC class I ...T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / negative regulation of Notch signaling pathway / 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 / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / 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 / 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 / histone deacetylase binding / negative regulation of neurogenesis / 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 / positive regulation of type II interferon production / 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 / 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 / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / early endosome membrane / late endosome membrane / T cell receptor signaling pathway / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / Golgi membrane / endoplasmic reticulum lumen / external side of plasma membrane / lysosomal membrane / innate immune response / focal adhesion / signaling receptor binding / endoplasmic reticulum membrane / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / negative regulation of transcription by RNA polymerase II 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.8 Å | ||||||
データ登録者 | Kumar, P. / Vahedi-Faridi, A. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. | ||||||
引用 | ジャーナル: Protein Sci. / 年: 2009 タイトル: Conformational changes within the HLA-A1:MAGE-A1 complex induced by binding of a recombinant antibody fragment with TCR-like specificity 著者: Kumar, P. / Vahedi-Faridi, A. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. #1: ジャーナル: J.Biol.Chem. / 年: 2005 タイトル: A major histocompatibility complex-peptide-restricted antibody and t cell receptor molecules recognize their target by distinct binding modes: crystal structure of human leukocyte ...タイトル: A major histocompatibility complex-peptide-restricted antibody and t cell receptor molecules recognize their target by distinct binding modes: crystal structure of human leukocyte antigen (HLA)-A1-MAGE-A1 in complex with FAB-HYB3 著者: Hulsmeyer, M. / Chames, P. / Hillig, R.C. / Stanfield, R.L. / Held, G. / Coulie, P.G. / Alings, C. / Wille, G. / Saenger, W. / Uchanska-Ziegler, B. / Hoogenboom, H.R. / Ziegler, A. | ||||||
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 | 3bo8.cif.gz | 109 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3bo8.ent.gz | 81.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3bo8.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/bo/3bo8 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/3bo8 | HTTPS FTP |
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-関連構造データ
関連構造データ | 1w72S S: 精密化の開始モデル |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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1 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 31636.955 Da / 分子数: 1 断片: Ectodomain, Alpha-1, Alpha-2, Alpha-3, UNP Residues 25-298 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) / 株 (発現宿主): BL21DE3 / 参照: UniProt: P30443, UniProt: P04439*PLUS | ||
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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) / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): XA90 / 参照: UniProt: P61769 | ||
#3: タンパク質・ペプチド | 分子量: 976.964 Da / 分子数: 1 / 断片: UNP Residues 161-169 / 由来タイプ: 合成 詳細: solid phase synthesis; This sequence occurs naturally in humans. 参照: UniProt: P43355 | ||
#4: 化合物 | #5: 水 | ChemComp-HOH / | |
-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: 2.68 Å3/Da / 溶媒含有率: 54.14 % |
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結晶化 | 温度: 291 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5 詳細: 20% PEG 3350, 0.2M Sodium Fluoride, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-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: BESSY / ビームライン: 14.1 / 波長: 0.954 Å |
検出器 | タイプ: MARRESEARCH / 検出器: CCD / 日付: 2005年5月20日 / 詳細: mirror |
放射 | モノクロメーター: Si-111 crystal / 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: 0.954 Å / 相対比: 1 |
反射 | 解像度: 1.8→63.888 Å / Num. obs: 43828 / % possible obs: 97 % / 冗長度: 4.1 % / Biso Wilson estimate: 18.248 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 17.3 |
反射 シェル | 解像度: 1.8→1.9 Å / 冗長度: 4 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 3.82 / Num. measured all: 24361 / Num. unique all: 6163 / Rsym value: 0.351 / % possible all: 95 |
-位相決定
位相決定 | 手法: 分子置換 | |||||||||
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Phasing MR | Rfactor: 0.431 / Cor.coef. Fo:Fc: 0.528
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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 1W72 解像度: 1.8→19.65 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.923 / SU B: 2.672 / SU ML: 0.084 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.125 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 19.157 Å2
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精密化ステップ | サイクル: LAST / 解像度: 1.8→19.65 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.8→1.847 Å / Total num. of bins used: 20
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