+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1bd2 | ||||||
---|---|---|---|---|---|---|---|
タイトル | COMPLEX BETWEEN HUMAN T-CELL RECEPTOR B7, VIRAL PEPTIDE (TAX) AND MHC CLASS I MOLECULE HLA-A 0201 | ||||||
要素 |
| ||||||
キーワード | COMPLEX (MHC/VIRAL PEPTIDE/RECEPTOR) / COMPLEX (MHC-VIRAL PEPTIDE-RECEPTOR) / COMPLEX (MHC-VIRAL PEPTIDE-RECEPTOR) complex | ||||||
機能・相同性 | 機能・相同性情報 MHC protein binding / symbiont-mediated perturbation of host exit from mitosis / : / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent ...MHC protein binding / symbiont-mediated perturbation of host exit from mitosis / : / symbiont-mediated perturbation of host cell cycle G0/G1 transition checkpoint / T cell receptor complex / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / Generation of second messenger molecules / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / PD-1 signaling / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / regulation of immune response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / regulation of mRNA stability / detection of bacterium / T cell receptor binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / 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 / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / 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 / SH3 domain binding / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / positive regulation of cellular senescence / 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 / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / host cell cytoplasm / amyloid fibril formation / 獲得免疫系 / learning or memory 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Human T-lymphotropic virus 1 (ウイルス) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.5 Å | ||||||
データ登録者 | Ding, Y.-H. / Smith, K.J. / Garboczi, D.N. / Utz, U. / Biddison, W.E. / Wiley, D.C. | ||||||
引用 | ジャーナル: Immunity / 年: 1998 タイトル: Two human T cell receptors bind in a similar diagonal mode to the HLA-A2/Tax peptide complex using different TCR amino acids. 著者: Ding, Y.H. / Smith, K.J. / Garboczi, D.N. / Utz, U. / Biddison, W.E. / Wiley, D.C. #1: ジャーナル: Nature / 年: 1996 タイトル: Structure of the Complex between Human T-Cell Receptor, Viral Peptide and Hla-A2 著者: Garboczi, D.N. / Ghosh, P. / Utz, U. / Fan, Q.R. / Biddison, W.E. / Wiley, D.C. | ||||||
履歴 |
|
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
---|
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1bd2.cif.gz | 169.6 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb1bd2.ent.gz | 134.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1bd2.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/bd/1bd2 ftp://data.pdbj.org/pub/pdb/validation_reports/bd/1bd2 | HTTPS FTP |
---|
-関連構造データ
-リンク
-集合体
登録構造単位 |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
単位格子 |
|
-要素
-タンパク質 , 2種, 2分子 AB
#1: タンパク質 | 分子量: 31854.203 Da / 分子数: 1 / 断片: EXTRACELLULAR DOMAINS ALPHA 1, ALPHA 2, ALPHA 3 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 細胞株: BL21 / 細胞内の位置: PLASMA MEMBRANE細胞膜 / 遺伝子: HLA-A 0201 / 器官: PLASMA / プラスミド: PHN1 細胞内の位置 (発現宿主): REFOLDED FROM INCLUSION BODIES 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): XA90 / 参照: UniProt: P01892, UniProt: P04439*PLUS |
---|---|
#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) / 細胞株: BL21 / 細胞内の位置: EXTRACELLULARGlossary of biology / 遺伝子: V BETA 12.3 J BETA 2.7 (BV13S1) / 器官: PLASMA / プラスミド: PLM1 / 生物種 (発現宿主): Escherichia coli 細胞内の位置 (発現宿主): REFOLDED FROM INCLUSION BODIES 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: UniProt: P61769 |
-T CELL RECEPTOR ... , 2種, 2分子 DE
#4: タンパク質 | 分子量: 22730.295 Da / 分子数: 1 / 断片: EXTRACELLULAR DOMAINS V AND C, RESIDUES 1 - 210 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / Cell: T-LYMPHOCYTE / 細胞株: BL21 / 細胞内の位置: PLASMA MEMBRANE細胞膜 / 遺伝子: V ALPHA 17.2, J ALPHA 54 (ADV21S1A1N2) / 器官: PLASMA / プラスミド: PLM1 / 生物種 (発現宿主): Escherichia coli 細胞内の位置 (発現宿主): REFOLDED FROM INCLUSION BODIES 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: GenBank: 338766, UniProt: P04437*PLUS |
---|---|
#5: タンパク質 | 分子量: 27326.229 Da / 分子数: 1 / 断片: EXTRACELLULAR DOMAINS V AND C, RESIDUES 1 - 247 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / Cell: T-LYMPHOCYTE / 細胞株: BL21 / 細胞内の位置: PLASMA MEMBRANE細胞膜 / 遺伝子: V BETA 12.3, J BETA 2.7 (BV13S1) / 器官: PLASMA / プラスミド: PLM1 / 生物種 (発現宿主): Escherichia coli 細胞内の位置 (発現宿主): REFOLDED FROM INCLUSION BODIES 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: GenBank: 3002925, UniProt: A0A0K0K1A5*PLUS |
-タンパク質・ペプチド / 非ポリマー , 2種, 40分子 C
#3: タンパク質・ペプチド | 分子量: 1070.280 Da / 分子数: 1 断片: RESIDUES 11 - 19 FROM TAX PROTEIN OF HUMAN T LYMPHOTROPIC VIRUS TYPE 1 由来タイプ: 組換発現 由来: (組換発現) Human T-lymphotropic virus 1 (ウイルス) 属: Deltaretrovirusデルタレトロウイルス属 / 生物種: Primate T-lymphotropic virus 1 / 参照: UniProt: P14079*PLUS |
---|---|
#6: 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 |
---|
-試料調製
結晶 | マシュー密度: 2.68 Å3/Da / 溶媒含有率: 58 % |
---|---|
結晶化 | pH: 7.1 詳細: 12% PEG8000, 20MM MOPS, 100MM MAGNESIUM ACETATE,PH7.1 |
-データ収集
回折 | 平均測定温度: 100 K |
---|---|
放射光源 | 由来: シンクロトロン / サイト: CHESS / ビームライン: A1 / 波長: 0.908 |
検出器 | タイプ: ADSC QUANTUM / 検出器: CCD / 日付: 1997年2月5日 |
放射 | 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 0.908 Å / 相対比: 1 |
反射 | 解像度: 2.5→20 Å / Num. obs: 33899 / % possible obs: 91.2 % / Observed criterion σ(I): -3 / 冗長度: 4.2 % / Biso Wilson estimate: 59.1 Å2 / Rmerge(I) obs: 0.11 |
反射 シェル | 解像度: 2.5→2.59 Å / Rmerge(I) obs: 0.22 / % possible all: 85.1 |
反射 | *PLUS Num. measured all: 145021 |
反射 シェル | *PLUS % possible obs: 85.1 % |
-解析
ソフトウェア |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRIES 1HHI AND 1AO7 解像度: 2.5→8 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1000000 / Data cutoff low absF: 1.0E-5 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 41.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.5→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 2.5→2.61 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ソフトウェア | *PLUS 名称: X-PLOR / バージョン: 3.851 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
|