+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1fzm | |||||||||
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タイトル | MHC CLASS I NATURAL MUTANT H-2KBM8 HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND VESICULAR STOMATITIS VIRUS NUCLEOPROTEIN | |||||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / major histocompatibility complex peptide-MHC | |||||||||
機能・相同性 | 機能・相同性情報 TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction ...TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / helical viral capsid / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / inner ear development / positive regulation of natural killer cell proliferation / 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 / positive regulation of immunoglobulin production / 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 interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / 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 / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / lumenal side of endoplasmic reticulum membrane / peptide binding / 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 / 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 / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / viral nucleocapsid / cellular response to lipopolysaccharide / intracellular iron ion homeostasis 類似検索 - 分子機能 | |||||||||
生物種 | Mus musculus (ハツカネズミ) | |||||||||
手法 | X線回折 / シンクロトロン / CNS, done by rigid body refinement of starting model. / 解像度: 1.8 Å | |||||||||
データ登録者 | Rudolph, M.G. / Speir, J.A. / Brunmark, A. / Mattsson, N. / Jackson, M.R. / Peterson, P.A. / Teyton, L. / Wilson, I.A. | |||||||||
引用 | ジャーナル: Immunity / 年: 2001 タイトル: The crystal structures of K(bm1) and K(bm8) reveal that subtle changes in the peptide environment impact thermostability and alloreactivity. 著者: Rudolph, M.G. / Speir, J.A. / Brunmark, A. / Mattsson, N. / Jackson, M.R. / Peterson, P.A. / Teyton, L. / Wilson, I.A. | |||||||||
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 | 1fzm.cif.gz | 96.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1fzm.ent.gz | 77.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1fzm.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/fz/1fzm ftp://data.pdbj.org/pub/pdb/validation_reports/fz/1fzm | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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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: 31587.264 Da / 分子数: 1 / 断片: EXTRACELLULAR DOMAIN / 変異: Y22F, M23I, E24S, D30N / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) 発現宿主: Drosophila melanogaster (キイロショウジョウバエ) 参照: UniProt: P01901 |
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#2: タンパク質 | 分子量: 11704.359 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) 発現宿主: Drosophila melanogaster (キイロショウジョウバエ) 参照: UniProt: P01887 |
-タンパク質・ペプチド , 1種, 1分子 P
#3: タンパク質・ペプチド | 分子量: 956.078 Da / 分子数: 1 / 断片: RESIDUES 52-59 / 由来タイプ: 合成 詳細: The peptide was chemically synthesized. The sequence of the peptide is found naturally in Vesicular stomatitis virus. 参照: UniProt: P11212 |
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-糖 , 2種, 2分子
#4: 多糖 | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose |
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#5: 糖 | ChemComp-NAG / |
-非ポリマー , 4種, 281分子
#6: 化合物 | #7: 化合物 | ChemComp-MRD / ( | #8: 化合物 | #9: 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: 3 Å3/Da / 溶媒含有率: 58 % | ||||||||||||||||||||||||
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結晶化 | 温度: 290 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.4 詳細: K/Na phosphate, MPD , pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 290K | ||||||||||||||||||||||||
結晶化 | *PLUS 温度: 17 ℃ | ||||||||||||||||||||||||
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: シンクロトロン / サイト: SSRL / ビームライン: BL9-2 / 波長: 0.98 |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD |
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: 0.98 Å / 相対比: 1 |
反射 | 解像度: 1.8→22.1 Å / Num. all: 49672 / Num. obs: 49672 / % possible obs: 95.1 % / Observed criterion σ(I): 2.5 / 冗長度: 2.9 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 23.2 |
反射 シェル | 解像度: 1.8→1.82 Å / 冗長度: 2.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1565 / % possible all: 91.9 |
反射 シェル | *PLUS % possible obs: 91.9 % / Num. unique obs: 1565 |
-解析
ソフトウェア |
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精密化 | 構造決定の手法: CNS, done by rigid body refinement of starting model. 開始モデル: pdb-entry 2vaa without peptide, water, and mutated side chains truncated to alanine. 解像度: 1.8→22.07 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 56662868.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / 交差検証法: THROUGHOUT / σ(F): 0 / σ(I): 0 / 立体化学のターゲット値: Engh & Huber
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溶媒の処理 | 溶媒モデル: FLAT MODEL / Bsol: 57.58 Å2 / ksol: 0.391 e/Å3 | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 30.9 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: 1.8→22.07 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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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: 1 / 分類: refinement | ||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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