+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1m05 | ||||||
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タイトル | HLA B8 in complex with an Epstein Barr Virus determinant | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / MHC class I (MHCクラスI分子) / HLA B8 / Epstein Barr virus (エプスタイン・バール・ウイルス) | ||||||
機能・相同性 | 機能・相同性情報 host cell nuclear matrix / DNA-templated viral transcription / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / 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 ...host cell nuclear matrix / DNA-templated viral transcription / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / 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 / 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 / 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 / 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 / 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 / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / 小胞体 / ゴルジ体 / signaling receptor binding / focal adhesion / 自然免疫系 / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / ゴルジ体 / 細胞膜 / 小胞体 / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / 生体膜 / identical protein binding / 細胞膜 / 細胞質基質 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 1.9 Å | ||||||
データ登録者 | Kjer-Nielsen, L. / Clements, C.S. / Brooks, A.G. / Purcell, A.W. / Fontes, M.R. / McCluskey, J. / Rossjohn, J. | ||||||
引用 | ジャーナル: J.IMMUNOL. / 年: 2003 タイトル: The structure of HLA-B8 complexed to an immunodominant viral determinant: peptide-induced conformational changes and a mode of MHC class I dimerization. 著者: Kjer-Nielsen, L. / Clements, C.S. / Brooks, A.G. / Purcell, A.W. / Fontes, M.R. / McCluskey, J. / Rossjohn, J. | ||||||
履歴 |
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Remark 999 | SEQUENCE ACCORDING TO THE AUTHOR, THIS IS A SITE OF POLYMORPHISM IN THE EBNA 3 ANTIGEN. THE 9-MER ...SEQUENCE ACCORDING TO THE AUTHOR, THIS IS A SITE OF POLYMORPHISM IN THE EBNA 3 ANTIGEN. THE 9-MER PEPTIDE THAT WAS SYNTHESIZED HAD LEU IN THE 9TH POSITION. |
-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 | 1m05.cif.gz | 176.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1m05.ent.gz | 147 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1m05.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/m0/1m05 ftp://data.pdbj.org/pub/pdb/validation_reports/m0/1m05 | HTTPS FTP |
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-関連構造データ
関連構造データ | 1agbS 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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2 |
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単位格子 |
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詳細 | HLA B8 is a heterodimeric receptor |
-要素
#1: タンパク質 | 分子量: 32015.055 Da / 分子数: 2 / 断片: residues 25-301 / 由来タイプ: 組換発現 / 詳細: truncation mutant / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P30460, UniProt: P01889*PLUS #2: タンパク質 | 分子量: 11748.160 Da / 分子数: 2 / 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: 1054.247 Da / 分子数: 2 / 断片: residues 193-201 / 由来タイプ: 合成 詳細: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PROTEIN IS NATURALLY FOUND IN EPSTEIN-BARR VIRUS. 参照: UniProt: P12977 #4: 化合物 | #5: 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: 2.69 Å3/Da / 溶媒含有率: 54.24 % | ||||||||||||||||||||||||||||||||||||||||||
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結晶化 | 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: VAPOR DIFFUSION, HANGING DROP | ||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ / pH: 5.6 / 手法: 蒸気拡散法, ハンギングドロップ法 | ||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-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: 回転陽極 / タイプ: RIGAKU RU300 / 波長: 1.5418 |
検出器 | 日付: 2002年3月15日 |
放射 | モノクロメーター: osmic mirrors / 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: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 1.9→20 Å / Num. obs: 76165 / Observed criterion σ(I): 0 |
反射 | *PLUS % possible obs: 99.1 % / 冗長度: 5.4 % / Num. measured all: 410938 / Rmerge(I) obs: 0.083 |
反射 シェル | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.306 |
-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 1AGB 解像度: 1.9→50 Å / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: Engh & Huber
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精密化ステップ | サイクル: LAST / 解像度: 1.9→50 Å
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精密化 | *PLUS % reflection Rfree: 4 % | |||||||||||||||||||||||||
溶媒の処理 | *PLUS | |||||||||||||||||||||||||
原子変位パラメータ | *PLUS | |||||||||||||||||||||||||
拘束条件 | *PLUS
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