+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3i6k | ||||||
---|---|---|---|---|---|---|---|
タイトル | Newly identified epitope from SARS-CoV membrane protein complexed with HLA-A*0201 | ||||||
要素 |
| ||||||
キーワード | IMMUNE SYSTEM / HLA-A2 / SARS-CoV / Membrane glycoprotein / Disulfide bond / Glycoprotein / Host-virus interaction / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Disease mutation / Glycation / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted / Envelope protein / Golgi apparatus / Viral matrix protein / Virion | ||||||
機能・相同性 | 機能・相同性情報 Maturation of protein M / Translation of Structural Proteins / Virion Assembly and Release / 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 ...Maturation of protein M / Translation of Structural Proteins / Virion Assembly and Release / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class I / host cell Golgi membrane / 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 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Attachment and Entry / 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 / 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 / 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 / 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 / SARS-CoV-1 activates/modulates innate immune responses / 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 / late endosome membrane / T cell receptor signaling pathway / iron ion transport / ER-Phagosome pathway / antibacterial humoral response / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / structural constituent of virion / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / innate immune response / focal adhesion 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) SARS coronavirus TJF (SARSコロナウイルス) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 2.8 Å | ||||||
データ登録者 | Liu, J. / Sun, Y. / Qi, J. / Chu, F. / Wu, H. / Gao, F. / Li, T. / Yan, J. / Gao, G.F. | ||||||
引用 | ジャーナル: J Infect Dis / 年: 2010 タイトル: The membrane protein of severe acute respiratory syndrome coronavirus acts as a dominant immunogen revealed by a clustering region of novel functionally and structurally defined ...タイトル: The membrane protein of severe acute respiratory syndrome coronavirus acts as a dominant immunogen revealed by a clustering region of novel functionally and structurally defined cytotoxic T-lymphocyte epitopes 著者: Liu, J. / Sun, Y. / Qi, J. / Chu, F. / Wu, H. / Gao, F. / Li, T. / Yan, J. / Gao, G.F. | ||||||
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 | 3i6k.cif.gz | 169.3 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb3i6k.ent.gz | 133.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3i6k.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/i6/3i6k ftp://data.pdbj.org/pub/pdb/validation_reports/i6/3i6k | HTTPS FTP |
---|
-関連構造データ
-リンク
-集合体
登録構造単位 |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
単位格子 |
|
-要素
#1: タンパク質 | 分子量: 31854.203 Da / 分子数: 2 / 断片: alpha 1-3 regions, UNP residues 25-299 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) 遺伝子: HLA-A, HLA-A*0201 allele, HLAA, Homo sapiens MHC class I antigen (HLA-A) プラスミド: pET28b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: UniProt: P01892, UniProt: P04439*PLUS #2: タンパク質 | 分子量: 11879.356 Da / 分子数: 2 / 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-microglobulin, CDABP0092, HDCMA22P / プラスミド: pGMT7 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 (DE3) / 参照: UniProt: P61769 #3: タンパク質・ペプチド | 分子量: 1007.246 Da / 分子数: 2 / 断片: UNP residue 60-69 / 由来タイプ: 合成 / 詳細: chemical synthesized 由来: (合成) SARS coronavirus TJF (SARSコロナウイルス) 参照: UniProt: Q692E0, UniProt: P59596*PLUS #4: 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: 2.67 Å3/Da / 溶媒含有率: 53.93 % |
---|---|
結晶化 | 温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 5.5 詳細: 0.1M BIS-TRIS pH 5.5, 10% w/v Polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-データ収集
回折 | 平均測定温度: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
放射光源 | 由来: 回転陽極 / タイプ: RIGAKU MICROMAX-007 / 波長: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
検出器 | タイプ: RIGAKU RAXIS VII / 検出器: IMAGE PLATE / 日付: 2008年9月14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: 1.54178 Å / 相対比: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Av R equivalents: 0.17 / 数: 173044 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 | 解像度: 2.75→32.209 Å / Num. obs: 25460 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / 冗長度: 6.8 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.17 / Rrim(I) all: 0.17 / Rsym value: 0.17 / Χ2: 2.156 / Net I/σ(I): 15.836 / Num. measured all: 173044 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
反射 シェル |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Cell measurement | Reflection used: 173044 |
-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 ENTRY 1JF1 解像度: 2.8→32.209 Å / Occupancy max: 1 / Occupancy min: 0.61 / FOM work R set: 0.845 / SU ML: 0.29 / σ(F): 0.11 / 位相誤差: 22.23 / 立体化学のターゲット値: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL / Bsol: 19.509 Å2 / ksol: 0.331 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso max: 114.13 Å2 / Biso mean: 35.595 Å2 / Biso min: 12.68 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.8→32.209 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル |
|