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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: 1seb | ||||||
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タイトル | COMPLEX OF THE HUMAN MHC CLASS II GLYCOPROTEIN HLA-DR1 AND THE BACTERIAL SUPERANTIGEN SEB | ||||||
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![]() | COMPLEX (MHC II/PEPTIDE/TOXIN) / HISTOCOMPATIBILITY ANTIGEN / MHC II / SUPERANTIGEN / ENTEROTOXIN PEPTIDE / TOXIN / COMPLEX (MHC II-PEPTIDE-TOXIN) COMPLEX | ||||||
機能・相同性 | ![]() regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / T cell receptor binding / detection of bacterium / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / toxin activity / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of protein phosphorylation / immune response / lysosomal membrane / external side of plasma membrane / Golgi membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() | ||||||
手法 | ![]() ![]() | ||||||
![]() | Jardetzky, T.S. / Brown, J.H. / Gorga, J.C. / Stern, L.J. / Urban, R.G. / Chi, Y.I. / Stauffacher, C. / Strominger, J.L. / Wiley, D.C. | ||||||
![]() | ![]() タイトル: Three-dimensional structure of a human class II histocompatibility molecule complexed with superantigen. 著者: Jardetzky, T.S. / Brown, J.H. / Gorga, J.C. / Stern, L.J. / Urban, R.G. / Chi, Y.I. / Stauffacher, C. / Strominger, J.L. / Wiley, D.C. #1: ![]() タイトル: Crystallographic Analysis of Endogenous Peptides Associated with Hla-Dr1 Suggests a Common, Polyproline II-Like Conformation for Bound Peptides 著者: Jardetzky, T.S. / Brown, J.H. / Gorga, J.C. / Stern, L.J. / Urban, R.G. / 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: ![]() ![]() |
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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 | ![]() | 233.7 KB | 表示 | ![]() |
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PDB形式 | ![]() | 197.5 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 | ![]() | 410.2 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 448.5 KB | 表示 | |
XML形式データ | ![]() | 27.9 KB | 表示 | |
CIF形式データ | ![]() | 42.8 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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非結晶学的対称性 (NCS) | NCS oper:
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詳細 | THE ASYMMETRIC UNIT CONTAINS A DIMER CONSISTING OF TWO HLA/DR-1 AND TWO SEB MOLECULES. THE DEPOSITORS PROVIDED A MONOMER AND THE TRANSFORMATIONS TO GENERATE THE OTHER MONOMER IN THE DIMER. THE PROTEIN DATA BANK GENERATED THE COMPLETE ASYMMETRIC UNIT USING THE TRANSFORMATIONS PROVIDED. CHAINS A, B, C, D WERE DEPOSITED AND CHAINS E, F, G, H WERE GENERATED USING THE TRANSFORMATIONS GIVEN ON MTRIX RECORDS BELOW. SEE REMARK 295 FOR ADDITIONAL DETAILS. |
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要素
#1: タンパク質 | 分子量: 21084.826 Da / 分子数: 2 / 断片: EXTRACELLULAR DOMAIN / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() #2: タンパク質 | 分子量: 22324.938 Da / 分子数: 2 / 断片: EXTRACELLULAR DOMAIN / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() #3: タンパク質・ペプチド | 分子量: 1124.378 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: SUPERPOSITION OF MANY DIFFERENT PEPTIDES / 由来: (天然) ![]() #4: タンパク質 | 分子量: 27793.309 Da / 分子数: 2 / 由来タイプ: 天然 由来: (天然) ![]() ![]() 細胞株: LG-2 / 参照: UniProt: P01552 |
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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: 2.82 Å3/Da / 溶媒含有率: 55 % | ||||||||||||||||||||||||||||||
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結晶 | *PLUS | ||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 25 ℃ / pH: 7.5 / 手法: 蒸気拡散法 | ||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
放射光源 | 由来: ![]() ![]() ![]() |
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検出器 | タイプ: KODAK / 検出器: IMAGE PLATE / 日付: 1991年11月1日 |
放射 | 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 0.918 Å / 相対比: 1 |
反射 | Num. obs: 40627 / % possible obs: 86 % / 冗長度: 3.3 % / Rmerge(I) obs: 0.057 |
反射 | *PLUS 最高解像度: 2.7 Å / 最低解像度: 30 Å |
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解析
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精密化 | 解像度: 2.7→6 Å / σ(F): 2 詳細: THERE IS SOME EVIDENCE THAT THE SECOND SEB MOLECULE IS FOUND AT LOWER OCCUPANCY IN THE LATTICE. THE DR1:SEB STRUCTURE CONTAINS A BACKBONE MODEL (REFINED AS POLYALANINE) FOR ELECTRON DENSITY ...詳細: THERE IS SOME EVIDENCE THAT THE SECOND SEB MOLECULE IS FOUND AT LOWER OCCUPANCY IN THE LATTICE. THE DR1:SEB STRUCTURE CONTAINS A BACKBONE MODEL (REFINED AS POLYALANINE) FOR ELECTRON DENSITY THAT CORRESPONDS TO A COMPLEX MIXTURE OF PEPTIDES THAT CO-PURIFY WITH THE HLA-DR1 MOLECULE (SEE REFERENCE 1 ABOVE FOR DETAILS). MHC CLASS II MOLECULES FORM VERY STABLE COMPLEXES WITH PEPTIDES AND, WHEN ISOLATED FROM HUMAN CELL LINES, HLA-DR1 MOLECULES HAVE BEEN SHOWN TO BE LOADED WITH A MIXTURE OF CELLULAR OR SERUM DERIVED PEPTIDES. THE NUMBER OF DIFFERENT PEPTIDES IS ESTIMATED TO BE ON THE ORDER OF THOUSANDS OF DIFFERENT SPECIES. IN THE CO-CRYSTAL OF HLA-DR1 WITH SEB, INTERPRETABLE ELECTRON DENSITY IS OBSERVED FOR THE BACKBONE OF A 13 AMINO ACID PEPTIDE WITH THE HLA-DR1 PEPTIDE-BINDING SITE. ALTHOUGH GOOD SIDE CHAIN DENSITY IS OBSERVED WITHIN THIS REGION, THE ELECTRON DENSITY COULD NOT BE UNAMBIGUOUSLY CORRELATED WITH ANY OF THE SEQUENCES DETERMINED FOR PEPTIDES ELUTED FROM PURIFIED HLA-DR1. THE ELECTRON DENSITY IS CONSISTENT WITH THE SUPERPOSITION OF MANY PEPTIDES WITH DIFFERENT SEQUENCES THAT ASSUME A COMMON CONFORMATION WITHIN THE HLA-DR1 PEPTIDE-BINDING SITE. THE POLYALANINE MODEL, THEREFORE, REPRESENTS A CONSENSUS CONFORMATION FOR PEPTIDE-BINDING TO HLA-DR1. IN THIS ENTRY THIS CHAIN IS PRESENTED AS CHAIN C (AND G) WITH THE RESIDUES NAMED "UNK".
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精密化ステップ | サイクル: LAST / 解像度: 2.7→6 Å
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拘束条件 |
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