+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1w0v | ||||||
---|---|---|---|---|---|---|---|
タイトル | Crystal Structure Of HLA-B*2705 Complexed With the self-Peptide TIS from EGF-response factor 1 | ||||||
要素 |
| ||||||
キーワード | IMMUNE SYSTEM (免疫系) / MHC / MAJOR HISTOCOMPATIBILITY COMPLEX (主要組織適合遺伝子複合体) / HLA- B*2705 / MHC I | ||||||
機能・相同性 | 機能・相同性情報 negative regulation of mitotic cell cycle phase transition / regulation of B cell differentiation / somatic stem cell division / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / negative regulation of stem cell differentiation / M-decay: degradation of maternal mRNAs by maternally stored factors / cellular response to granulocyte macrophage colony-stimulating factor stimulus / regulation of interleukin-12 production / regulation of dendritic cell differentiation ...negative regulation of mitotic cell cycle phase transition / regulation of B cell differentiation / somatic stem cell division / 3'-UTR-mediated mRNA destabilization / mRNA 3'-UTR AU-rich region binding / negative regulation of stem cell differentiation / M-decay: degradation of maternal mRNAs by maternally stored factors / cellular response to granulocyte macrophage colony-stimulating factor stimulus / regulation of interleukin-12 production / regulation of dendritic cell differentiation / cellular response to fibroblast growth factor stimulus / definitive hemopoiesis / regulation of T cell anergy / cellular response to glucocorticoid stimulus / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / regulation of interleukin-6 production / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / negative regulation of fat cell differentiation / mRNA catabolic process / somatic stem cell population maintenance / 造血 / TAP binding / protection from natural killer cell mediated cytotoxicity / cellular response to epidermal growth factor stimulus / ERK1 and ERK2 cascade / 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 transforming growth factor beta stimulus / regulation of mRNA stability / detection of bacterium / secretory granule membrane / 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 / defense response / 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 / response to wounding / 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 / 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 / sensory perception of smell / regulation of translation / 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 / cellular response to tumor necrosis factor / positive regulation of protein binding / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / 獲得免疫系 / learning or memory / 免疫応答 / ribonucleoprotein complex 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: 2.27 Å | ||||||
データ登録者 | Hulsmeyer, M. / Fiorillo, M.T. / Bettosini, F. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 2005 タイトル: Thermodynamic and Structural Equivalence of Two Hla-B27 Subtypes Complexed with a Self-Peptide 著者: Hulsmeyer, M. / Welfle, K. / Pohlmann, T. / Misselwitz, R. / Alexiev, U. / Welfle, H. / Saenger, W. / Uchanska-Ziegler, B. / Ziegler, A. #1: ジャーナル: J.Exp.Med. / 年: 2004 タイトル: Dual, Hla-B27 Subtype-Dependent Conformation of a Self-Peptide 著者: Hulsmeyer, M. / Fiorillo, M.T. / Bettosini, F. / Sorrentino, R. / Saenger, W. / Ziegler, A. / Uchanska-Ziegler, B. #2: ジャーナル: J.Biol.Chem. / 年: 2004 タイトル: Thermodynamic and Structural Analysis of Peptide- and Allele-Dependent Properties of Two Hla-B27 Subtypes Exhibiting Differential Disease Association 著者: Hillig, R.C. / Hulsmeyer, M. / Saenger, W. / Welfle, K. / Misselwitz, R. / Welfle, H. / Kozerski, C. / Volz, A. / Uchanska-Ziegler, B. / Ziegler, A. | ||||||
履歴 |
| ||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-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 | 1w0v.cif.gz | 103.6 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb1w0v.ent.gz | 78.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1w0v.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/w0/1w0v ftp://data.pdbj.org/pub/pdb/validation_reports/w0/1w0v | 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
#1: タンパク質 | 分子量: 31928.160 Da / 分子数: 1 / 断片: EXTRACELLULAR DOMAIN, RESIDUES 25-300 / 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) / 参照: UniProt: P03989, UniProt: P01889*PLUS | ||||
---|---|---|---|---|---|
#2: タンパク質 | 分子量: 11879.356 Da / 分子数: 1 / 断片: RESIDUES 21-119 / 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) / 参照: UniProt: P61769 | ||||
#3: タンパク質・ペプチド | 分子量: 1160.436 Da / 分子数: 1 / 断片: RESIDUES 479-487 / 由来タイプ: 合成 / 由来: (合成) HOMO SAPIENS (ヒト) / 参照: UniProt: P47974 | ||||
#4: 化合物 | #5: 水 | ChemComp-HOH / | 構成要素の詳細 | BETA-2-MICROGLOBULIN IS THE BETA-CHAIN OF MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I MOLECULES. ...BETA-2-MICROGLOBU | |
-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: 2.7 Å3/Da / 溶媒含有率: 53 % |
---|---|
結晶化 | pH: 8 / 詳細: 18% PEG8000, 0.1M TRIS PH 8.0 |
-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: BESSY / ビームライン: 14.2 / 波長: 0.886 |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE / 日付: 2002年9月12日 / 詳細: MIRRORS |
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: 0.886 Å / 相対比: 1 |
反射 | 解像度: 2.27→29.6 Å / Num. obs: 20780 / % possible obs: 95 % / 冗長度: 3.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13 |
反射 シェル | 解像度: 2.27→2.35 Å / 冗長度: 2.3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.1 / % possible all: 88.4 |
-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 1JGE 解像度: 2.27→65.94 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.872 / SU B: 6.119 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / 交差検証法: THROUGHOUT / ESU R: 0.362 / ESU R Free: 0.248 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 mean: 25.57 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.27→65.94 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 |
|