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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 1qlf | ||||||
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タイトル | MHC CLASS I H-2DB COMPLEXED WITH GLYCOPEPTIDE K3G | ||||||
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![]() | IMMUNE SYSTEM/PEPTIDE / MURINE CLASS I MHC-PEPTIDE COMPLEX / MHC / GLYCOPEPTIDE / ANTIGEN / HISTOCOMPATIBILITY / IMMUNOLOGY / IMMUNE SYSTEM-PEPTIDE complex | ||||||
機能・相同性 | ![]() : / : / regulation of membrane depolarization / retina homeostasis / helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding ...: / : / regulation of membrane depolarization / retina homeostasis / helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin 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 / 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 / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / 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 / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of cellular senescence / peptide antigen binding / 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 / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / early endosome membrane / antibacterial humoral response / T cell differentiation in thymus / protein refolding / cellular response to lipopolysaccharide / viral nucleocapsid / protein homotetramerization / defense response to Gram-negative bacterium / intracellular iron ion homeostasis / amyloid fibril formation / host cell cytoplasm / learning or memory / defense response to Gram-positive bacterium / ribonucleoprotein complex / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / external side of plasma membrane / Golgi membrane / innate immune response / focal adhesion / signaling receptor binding / Neutrophil degranulation / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() ![]() | ||||||
手法 | ![]() ![]() ![]() | ||||||
![]() | Tormo, J. / Jones, E.Y. | ||||||
![]() | ![]() タイトル: Crystal Structures of Two H-2Db/Glycopeptide Complexes Suggest a Molecular Basis for Ctl Cross-Reactivity 著者: Glithero, A. / Tormo, J. / Haurum, J.S. / Arsequell, G. / Valencia, G. / Edwards, J. / Springer, S. / Townsend, A. / Pao, Y.-L. / Wormald, M. / Dwek, R.A. / Jones, E.Y. / Elliot, T. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 97.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 72.6 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 419 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 426.4 KB | 表示 | |
XML形式データ | ![]() | 10.1 KB | 表示 | |
CIF形式データ | ![]() | 15.6 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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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: 32087.703 Da / 分子数: 1 / 断片: EXTRACELLULAR DOMAINS / 由来タイプ: 組換発現 詳細: FORMS HETEROTRIMER WITH CHAIN B (BETA-2-MICROGLOBULIN) AND CHAIN C (PEPTIDE ANTIGEN) 由来: (組換発現) ![]() ![]() 発現宿主: ![]() ![]() 参照: UniProt: P01899 |
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#2: タンパク質 | 分子量: 11748.160 Da / 分子数: 1 / 断片: MHC ASSOCIATED LIGHT CHAIN / 由来タイプ: 組換発現 / 詳細: FORMS HETEROTRIMER WITH CHAIN A AND CHAIN C / 由来: (組換発現) ![]() 発現宿主: ![]() ![]() 参照: UniProt: P01884, UniProt: P61769*PLUS |
-タンパク質・ペプチド / 糖 , 2種, 2分子 C![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#3: タンパク質・ペプチド | 分子量: 979.086 Da / 分子数: 1 / 断片: H-2DB-BOUND GLYCOPEPTIDE FROM NUCLEOCAPSID PROTEIN / 由来タイプ: 合成 詳細: PEPTIDE DERIVED FROM SENDAI VIRUS NUCLEOPROTEIN RESIDUES 324-332, GLY327 HAS BEEN REPLACED BY AN O-GLCNAC SUBSTITUTED SERINE 由来: (合成) ![]() |
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#6: 糖 | ChemComp-NAG / |
-非ポリマー , 3種, 163分子 ![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#4: 化合物 | #5: 化合物 | ChemComp-SO4 / | #7: 水 | ChemComp-HOH / | |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.8 Å3/Da / 溶媒含有率: 55 % | ||||||||||||||||||||||||||||||
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結晶化 | pH: 5 / 詳細: pH 5.00 | ||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 4 ℃ / pH: 7.5 / 手法: 蒸気拡散法, シッティングドロップ法 | ||||||||||||||||||||||||||||||
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: ![]() ![]() ![]() |
検出器 | タイプ: MARRESEARCH / 検出器: IMAGE PLATE |
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 Å / 相対比: 1 |
反射 | 解像度: 2.65→10 Å / Num. obs: 14363 / % possible obs: 97 % / Biso Wilson estimate: 39.3 Å2 / Rsym value: 0.06 |
反射 シェル | 解像度: 2.65→2.73 Å / Rsym value: 0.17 / % possible all: 95.1 |
反射 | *PLUS % possible obs: 97 % / Rmerge(I) obs: 0.06 |
反射 シェル | *PLUS % possible obs: 95.1 % / Rmerge(I) obs: 0.176 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: PDB ENTRY 1CE6 解像度: 2.65→20 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 詳細: THE CARBOHYDRATE ATTACHED TO THE GLYCOPEPTIDE IS DISORDERED. ONLY ONE OF THE TWO MAJOR CONFORMATIONS HAS BEEN MODELLED WITH HALF OCCUPANCY.
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 23.7963 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 33.7 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.65→20 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.65→2.74 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
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Xplor file |
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ソフトウェア | *PLUS 名称: CNS / バージョン: 0.5 / 分類: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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