+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1tmc | ||||||
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タイトル | THE THREE-DIMENSIONAL STRUCTURE OF A CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX MOLECULE MISSING THE ALPHA3 DOMAIN OF THE HEAVY CHAIN | ||||||
要素 |
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キーワード | HISTOCOMPATIBILITY ANTIGEN | ||||||
機能・相同性 | 機能・相同性情報 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 / 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 CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding ...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 / 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 CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / endoplasmic reticulum exit site / beta-2-microglobulin binding / 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 / T cell receptor 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 / 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 / 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 / positive regulation of type II interferon production / sensory perception of smell / E3 ubiquitin ligases ubiquitinate target proteins / 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 / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein refolding / early endosome membrane / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / 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 / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / ゴルジ体 / 細胞膜 / 小胞体 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 解像度: 2.3 Å | ||||||
データ登録者 | Collins, E.J. / Garboczi, D.N. / Karpusas, M.N. / Wiley, D.C. | ||||||
引用 | ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 1995 タイトル: The three-dimensional structure of a class I major histocompatibility complex molecule missing the alpha 3 domain of the heavy chain. 著者: Collins, E.J. / Garboczi, D.N. / Karpusas, M.N. / Wiley, D.C. #1: ジャーナル: J.Mol.Biol. / 年: 1994 タイトル: Five Viral Peptide-Hla-A2 Co-Crystals: Simultaneous Space Group Determination and X-Ray Data Collection 著者: Garboczi, D.N. / Madden, D.R. / Wiley, D.C. #2: ジャーナル: Cell(Cambridge,Mass.) / 年: 1993 タイトル: The Antigenic Identity of Peptide-Mhc Complexes: A Comparison of the Conformations of Five Viral Peptides Presented by Hla-A2 著者: Madden, D.R. / Garboczi, D.N. / Wiley, D.C. #3: ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 1993 タイトル: Comparison of the P2 Specificity Pocket in Three Human Histocompatibility Antigens: Hla-A(Asterisk)6801,Hla-A(Asterisk)0201, and Hla-B(Asterisk)2705 著者: Guo, H.-C. / Madden, D.R. / Silver, M.L. / Jardetzky, T.S. / Gorga, J.C. / Strominger, J.L. / Wiley, D.C. #4: ジャーナル: Nature / 年: 1992 タイトル: Different Length Peptides Bind to Hla-Aw68 Similarly at Their Ends But Bulge Out in the Middle 著者: Guo, H.-C. / Jardetzky, T.S. / Garrett, T.P.J. / Lane, W.S. / Strominger, J.L. / Wiley, D.C. #5: ジャーナル: Proc.Natl.Acad.Sci.USA / 年: 1992 タイトル: Hla-A2-Peptide Complexes: Refolding and Crystallization of Molecules Expressed in Escherichia Coli and Complexed with Single Antigenic Peptides 著者: Garboczi, D.N. / Hung, D.T. / Wiley, D.C. #6: ジャーナル: J.Mol.Biol. / 年: 1991 タイトル: Refined Structure of the Human Histocompatibility Antigen Hla-A2 at 2.6 Angstroms Resolution 著者: Saper, M.A. / Bjorkman, P.J. / Wiley, D.C. #7: ジャーナル: Nature / 年: 1987 タイトル: Structure of the Human Class I Histocompatibility Antigen, Hla-A2 著者: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C. #8: ジャーナル: Nature / 年: 1987 タイトル: The Foreign Antigen Binding Site and T Cell Recognition Regions of Class I Histocompatibility Antigens 著者: Bjorkman, P.J. / Saper, M.A. / Samraoui, B. / Bennett, W.S. / Strominger, J.L. / Wiley, D.C. #9: ジャーナル: J.Mol.Biol. / 年: 1985 タイトル: Crystallization and X-Ray Diffraction Studies on the Histocompatibility Antigens Hla-A2 and Hla-A28 from Human Cell Membranes 著者: Bjorkman, P.J. / Strominger, J.L. / Wiley, D.C. | ||||||
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 | 1tmc.cif.gz | 67.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1tmc.ent.gz | 54.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1tmc.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/tm/1tmc ftp://data.pdbj.org/pub/pdb/validation_reports/tm/1tmc | 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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Atom site foot note | 1: CIS PROLINE - PRO B 32 |
-要素
#1: タンパク質 | 分子量: 20315.336 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BETA-2-MICROGLOBULIN / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P01891, UniProt: P04439*PLUS |
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#2: タンパク質 | 分子量: 11879.356 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: BETA-2-MICROGLOBULIN / 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: 1228.375 Da / 分子数: 1 / 由来タイプ: 合成 |
#4: 水 | ChemComp-HOH / |
-実験情報
-実験
実験 | 手法: X線回折 |
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-試料調製
結晶 | マシュー密度: 2.29 Å3/Da / 溶媒含有率: 46.36 % | |||||||||||||||||||||||||
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結晶化 | *PLUS pH: 6.5 / 手法: 蒸気拡散法 | |||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
放射 | 散乱光タイプ: x-ray |
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放射波長 | 相対比: 1 |
反射 | *PLUS 最高解像度: 2.3 Å / 最低解像度: 20 Å / % possible obs: 99 % / Rmerge(I) obs: 0.07 |
反射 シェル | *PLUS 最高解像度: 2.3 Å / 最低解像度: 2.39 Å / Rmerge(I) obs: 0.228 |
-解析
ソフトウェア |
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精密化 | 解像度: 2.3→6 Å / Rfactor Rwork: 0.207 / Rfactor obs: 0.207 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.3→6 Å
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拘束条件 |
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精密化 | *PLUS Num. reflection all: 12084 / σ(I): 3 / Rfactor all: 0.227 / Rfactor Rfree: 0.304 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS タイプ: x_angle_d / Dev ideal: 1.92 |