+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1x7q | ||||||
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タイトル | Crystal structure of HLA-A*1101 with sars nucleocapsid peptide | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / PEPTIDE-MHC-COMPLEX / MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I (MHCクラスI分子) / MHC-I (MHCクラスI分子) / HUMAN LEUKOCYTE ANTIGEN (ヒト白血球型抗原) / HLA / IMMUNOGLOBULIN FAMILY (免疫グロブリンスーパーファミリー) / SARS (重症急性呼吸器症候群) | ||||||
機能・相同性 | 機能・相同性情報 SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / Maturation of nucleoprotein / SARS-CoV-1 modulates host translation machinery / 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 ...SARS-CoV-1-host interactions / Translation of Structural Proteins / Virion Assembly and Release / viral RNA genome packaging / Transcription of SARS-CoV-1 sgRNAs / negative regulation of interferon-beta production / Maturation of nucleoprotein / SARS-CoV-1 modulates host translation machinery / 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 / 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 / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / Attachment and Entry / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / 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 / detection of bacterium / T cell receptor binding / 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 / 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 / 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 / SARS-CoV-1 activates/modulates innate immune responses / antigen processing and presentation of exogenous peptide antigen via MHC class II / カプシド / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / negative regulation of epithelial cell proliferation / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / positive regulation of type II interferon production / sensory perception of smell / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / positive regulation of protein binding / ER-Phagosome pathway / antibacterial humoral response / iron ion transport / host cell endoplasmic reticulum-Golgi intermediate compartment / T cell receptor signaling pathway / protein refolding / early endosome membrane / host cell Golgi apparatus / viral nucleocapsid / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / molecular adaptor activity / host cell perinuclear region of cytoplasm 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: 1.45 Å | ||||||
データ登録者 | Blicher, T. / Kastrup, J.S. / Buus, S. / Gajhede, M. | ||||||
引用 | ジャーナル: Acta Crystallogr.,Sect.D / 年: 2005 タイトル: High-resolution structure of HLA-A*1101 in complex with SARS nucleocapsid peptide. 著者: Blicher, T. / Kastrup, J.S. / Buus, S. / Gajhede, M. | ||||||
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 | 1x7q.cif.gz | 202.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1x7q.ent.gz | 160.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1x7q.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/x7/1x7q ftp://data.pdbj.org/pub/pdb/validation_reports/x7/1x7q | HTTPS FTP |
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-関連構造データ
関連構造データ | 1hlaS 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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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: 31855.051 Da / 分子数: 1 / 断片: EXTRACELLULAR FRAGMENT / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: PET-28A / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: UniProt: P13746, UniProt: P04439*PLUS |
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#2: タンパク質 | 分子量: 11748.160 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: PET-28A / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: UniProt: P61769 |
-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: 1046.214 Da / 分子数: 1 / 由来タイプ: 合成 詳細: CHEMICALLY SYNTHESIZED PEPTIDE. THIS SEQUENCE OCCURS NATURALLY IN SARS CORONAVIRUS NUCLEOCAPSID PROTEIN, POSITION 362-370. 参照: UniProt: P59595 |
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-非ポリマー , 3種, 584分子
#4: 化合物 | #5: 化合物 | ChemComp-GOL / #6: 水 | ChemComp-HOH / | |
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-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: 2.07 Å3/Da / 溶媒含有率: 40.5 % |
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結晶化 | 温度: 293.15 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 6.5 詳細: 25% PEG 5000 MME, 0.2M AMMONIUM SULFATE, 0.1M MES PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K |
-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: 14.2 / 波長: 0.9815 / 波長: 0.9815 Å |
検出器 | タイプ: MARRESEARCH / 検出器: CCD / 日付: 2003年8月28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: 0.9815 Å / 相対比: 1 |
反射 | 解像度: 1.45→36 Å / Num. all: 81898 / Num. obs: 81898 / % possible obs: 100 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / 冗長度: 4.84 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 15.94 |
反射 シェル | 解像度: 1.45→1.48 Å / 冗長度: 3.94 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.14 / Num. unique all: 4079 / Rsym value: 0.45 / % possible all: 100 |
-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: 1HLA 解像度: 1.45→30 Å / Num. parameters: 34721 / Num. restraintsaints: 42247 / Isotropic thermal model: ANISOTROPIC / 交差検証法: THROUGHOUT / σ(F): 0 / 立体化学のターゲット値: Engh & Huber 詳細: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.29 %
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原子変位パラメータ | Biso mean: 23 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 20 / Occupancy sum hydrogen: 2823.81 / Occupancy sum non hydrogen: 3773.22 | |||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.45→30 Å
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拘束条件 |
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