+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5lax | ||||||
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タイトル | Crystal structure of HLA_DRB1*04:01 in complex with alpha-enolase peptide 26-40 | ||||||
要素 |
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キーワード | IMMUNE SYSTEM / HLA / autoimmune desease / rheumathoid arthritis / MHC class II | ||||||
機能・相同性 | 機能・相同性情報 negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / Manipulation of host energy metabolism / positive regulation of plasminogen activation / positive regulation of muscle contraction / regulation of interleukin-4 production / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation ...negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / Manipulation of host energy metabolism / positive regulation of plasminogen activation / positive regulation of muscle contraction / regulation of interleukin-4 production / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / 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 / Gluconeogenesis / positive regulation of monocyte differentiation / CD4 receptor binding / inflammatory response to antigenic stimulus / positive regulation of kinase activity / M band / canonical glycolysis / nuclear outer membrane / Glycolysis / intermediate filament / transport vesicle membrane / polysaccharide binding / T-helper 1 type immune response / positive regulation of ATP biosynthetic process / 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 / negative regulation of T cell proliferation / detection of bacterium / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / transcription corepressor binding / trans-Golgi network membrane / gluconeogenesis / glycolytic process / lumenal side of endoplasmic reticulum membrane / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein tetramerization / clathrin-coated endocytic vesicle membrane / response to virus / ER to Golgi transport vesicle membrane / negative regulation of cell growth / structural constituent of cytoskeleton / cognition / DNA-binding transcription repressor activity, RNA polymerase II-specific / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / transcription corepressor activity / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / GTPase binding / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / cell cortex / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / lysosome / cadherin binding / immune response / positive regulation of protein phosphorylation / external side of plasma membrane / Golgi membrane / lysosomal membrane / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / cell surface / magnesium ion binding / signal transduction / protein homodimerization activity / RNA binding / extracellular space 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.6 Å | ||||||
データ登録者 | Dubnovitsky, A. / Kozhukh, G. / Sandalova, T. / Achour, A. | ||||||
引用 | ジャーナル: Front Immunol / 年: 2016 タイトル: Functional and Structural Characterization of a Novel HLA-DRB1*04:01-Restricted alpha-Enolase T Cell Epitope in Rheumatoid Arthritis. 著者: Gerstner, C. / Dubnovitsky, A. / Sandin, C. / Kozhukh, G. / Uchtenhagen, H. / James, E.A. / Ronnelid, J. / Ytterberg, A.J. / Pieper, J. / Reed, E. / Tandre, C. / Rieck, M. / Zubarev, R.A. / ...著者: Gerstner, C. / Dubnovitsky, A. / Sandin, C. / Kozhukh, G. / Uchtenhagen, H. / James, E.A. / Ronnelid, J. / Ytterberg, A.J. / Pieper, J. / Reed, E. / Tandre, C. / Rieck, M. / Zubarev, R.A. / Ronnblom, L. / Sandalova, T. / Buckner, J.H. / Achour, A. / Malmstrom, V. | ||||||
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 | 5lax.cif.gz | 327.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5lax.ent.gz | 267.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5lax.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/la/5lax ftp://data.pdbj.org/pub/pdb/validation_reports/la/5lax | 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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単位格子 |
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非結晶学的対称性 (NCS) | NCSドメイン:
NCSドメイン領域: Component-ID: _ / Refine code: _
NCSアンサンブル:
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-要素
#1: タンパク質 | 分子量: 21911.750 Da / 分子数: 2 / 由来タイプ: 組換発現 詳細: Extracellular domain, UNP residues 26-206. ADLVPR ARE A PART OF EXPRESSION TAG 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-DRA, HLA-DRA1 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21 (DE3) / Variant (発現宿主): Star / 参照: UniProt: P01903 #2: タンパク質 | 分子量: 23102.672 Da / 分子数: 2 / 由来タイプ: 組換発現 詳細: Extracellular domain, UNP residues 26-206. ADLVPR ARE A PART OF EXPRESSION TAG 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HLA-DRB1 / 発現宿主: Escherichia coli / 株 (発現宿主): BL21 (DE3) / Variant (発現宿主): Star / 参照: UniProt: P13760, UniProt: P01911*PLUS #3: タンパク質・ペプチド | 分子量: 1450.640 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: synthetic construct (人工物) / 参照: UniProt: P06733*PLUS #4: 化合物 | ChemComp-MLA / | #5: 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: 1.98 Å3/Da / 溶媒含有率: 37.77 % |
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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 / pH: 4 詳細: 100 mM sodium malonate, pH 4.0, 12 to 18 percent (vol/vol) PEG3350 |
-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: BESSY / ビームライン: 14.1 / 波長: 0.918 Å |
検出器 | タイプ: DECTRIS PILATUS3 6M / 検出器: PIXEL / 日付: 2016年4月13日 |
放射 | モノクロメーター: Si-111 crystal / 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: 0.918 Å / 相対比: 1 |
反射 | 解像度: 2.6→48.2 Å / Num. obs: 138347 / % possible obs: 99.6 % / 冗長度: 5.9 % / Biso Wilson estimate: 38.6 Å2 / CC1/2: 0.989 / Net I/σ(I): 7.8 |
反射 シェル | 解像度: 2.6→2.75 Å / 冗長度: 6 % / Mean I/σ(I) obs: 1.8 / % possible all: 98.8 |
-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 開始モデル: 5JLZ 解像度: 2.6→47.56 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.877 / SU B: 31.692 / SU ML: 0.341 / 交差検証法: THROUGHOUT / ESU R Free: 0.389 / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 44.247 Å2
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精密化ステップ | サイクル: 1 / 解像度: 2.6→47.56 Å
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拘束条件 |
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