+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2fse | ||||||
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タイトル | Crystallographic structure of a rheumatoid arthritis MHC susceptibility allele, HLA-DR1 (DRB1*0101), complexed with the immunodominant determinant of human type II collagen | ||||||
要素 |
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キーワード | IMMUNE SYSTEM (免疫系) / STRUCTURAL PROTEIN (タンパク質) / rheumatoid arthritis (関節リウマチ) / HLA-DR1 / collagen type II / antigen presentation (抗原提示) | ||||||
機能・相同性 | 機能・相同性情報 collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / regulation of interleukin-4 production ...collagen type II trimer / collagen type XI trimer / anterior head development / embryonic skeletal joint morphogenesis / otic vesicle development / Collagen chain trimerization / proteoglycan metabolic process / extracellular matrix structural constituent conferring tensile strength / platelet-derived growth factor binding / regulation of interleukin-4 production / Extracellular matrix organization / notochord development / limb bud formation / regulation of interleukin-10 production / Collagen biosynthesis and modifying enzymes / cartilage development involved in endochondral bone morphogenesis / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / tissue homeostasis / MHC class II receptor activity / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell activation / Signaling by PDGF / cellular response to BMP stimulus / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / endochondral ossification / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / NCAM1 interactions / positive regulation of kinase activity / inflammatory response to antigenic stimulus / collagen fibril organization / cartilage development / 中間径フィラメント / proteoglycan binding / transport vesicle membrane / MET activates PTK2 signaling / Assembly of collagen fibrils and other multimeric structures / inner ear morphogenesis / T-helper 1 type immune response / polysaccharide binding / cartilage condensation / roof of mouth development / 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 / 液性免疫 / macrophage differentiation / Collagen degradation / negative regulation of type II interferon production / Generation of second messenger molecules / 免疫シナプス / Non-integrin membrane-ECM interactions / 基底膜 / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ECM proteoglycans / PD-1 signaling / epidermis development / Integrin cell surface interactions / chondrocyte differentiation / heart morphogenesis / negative regulation of inflammatory response to antigenic stimulus / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of T cell proliferation / MHC class II antigen presentation / 視覚 / detection of bacterium / T cell receptor binding / trans-Golgi network membrane / central nervous system development / skeletal system development / lumenal side of endoplasmic reticulum membrane / protein tetramerization / sensory perception of sound / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / 認識 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / 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 / Interferon gamma signaling / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / 遺伝子発現の調節 / collagen-containing extracellular matrix 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Mus musculus (ハツカネズミ) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 3.1 Å | ||||||
データ登録者 | Ivey, R.A. / Rosloniec, E.F. / Whittington, K.B. / Kang, A.H. / Park, H.W. | ||||||
引用 | ジャーナル: J.Immunol. / 年: 2006 タイトル: Crystallographic Structure of a Rheumatoid Arthritis MHC Susceptibility Allele, HLA-DR1 (DRB1*0101), Complexed with the Immunodominant Determinant of Human Type II Collagen. 著者: Rosloniec, E.F. / Ivey, R.A. / Whittington, K.B. / Kang, A.H. / Park, H.W. | ||||||
履歴 |
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Remark 999 | SEQUENCE THERE WAS NO SEQUENCE DATABASE REFERENCE AT THE TIME OF PROCESSING FOR THE MHC CHAINS. |
-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 | 2fse.cif.gz | 156.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2fse.ent.gz | 130.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2fse.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/fs/2fse ftp://data.pdbj.org/pub/pdb/validation_reports/fs/2fse | 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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2 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 20711.234 Da / 分子数: 2 / 由来タイプ: 組換発現 詳細: chains A and C form a chimera with chains B and D, respectively 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: pRmHA-3 発現宿主: Drosophila melanogaster (キイロショウジョウバエ) 参照: UniProt: P01903 #2: タンパク質 | 分子量: 21909.436 Da / 分子数: 2 / 由来タイプ: 組換発現 詳細: chains B and D form a chimera with chains A and C, respectively 由来: (組換発現) Mus musculus (ハツカネズミ) / プラスミド: pRmHA-3 発現宿主: Drosophila melanogaster (キイロショウジョウバエ) 参照: UniProt: P04229, UniProt: P01911*PLUS #3: タンパク質・ペプチド | 分子量: 1360.471 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: COL2A1 / プラスミド: pRmHA-3 発現宿主: Drosophila melanogaster (キイロショウジョウバエ) 参照: UniProt: P02458 #4: 水 | ChemComp-HOH / | |
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-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: 3.21 Å3/Da / 溶媒含有率: 61.7 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 詳細: 20% polyethylene glycol 3,350 and 200 mM ammonium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-データ収集
回折 | 平均測定温度: 77 K |
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放射光源 | 由来: シンクロトロン / サイト: APS / ビームライン: 22-ID / 波長: 1 Å |
検出器 | 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: 1 Å / 相対比: 1 |
反射 | 解像度: 3.1→91.287 Å / Num. all: 21330 / Num. obs: 20446 / % possible obs: 82.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / 冗長度: 2.9 % / Limit h max: 19 / Limit h min: 0 / Limit k max: 35 / Limit k min: 0 / Limit l max: 55 / Limit l min: 0 / Rsym value: 0.099 / Net I/σ(I): 11.4 |
反射 シェル | 解像度: 3.1→3.21 Å / 冗長度: 2.9 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2046 / Rsym value: 0.382 / % possible all: 96.7 |
-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 / 解像度: 3.1→20 Å / σ(F): 1936
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溶媒の処理 | Bsol: 15.01 Å2 | ||||||||||||||||
原子変位パラメータ | Biso mean: 26.877 Å2
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精密化ステップ | サイクル: LAST / 解像度: 3.1→20 Å
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Xplor file |
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