+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1yjd | ||||||
---|---|---|---|---|---|---|---|
タイトル | Crystal structure of human CD28 in complex with the Fab fragment of a mitogenic antibody (5.11A1) | ||||||
要素 |
| ||||||
キーワード | IMMUNE SYSTEM/SIGNALING PROTEIN (免疫系) / IgSF (免疫グロブリンスーパーファミリー) / CD28 homodimer / IMMUNE SYSTEM-SIGNALING PROTEIN COMPLEX (免疫系) | ||||||
機能・相同性 | 機能・相同性情報 Nef mediated downregulation of CD28 cell surface expression / positive regulation of inflammatory response to antigenic stimulus / regulatory T cell differentiation / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / CD4-positive, alpha-beta T cell proliferation / positive regulation of isotype switching to IgG isotypes / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / CD28 co-stimulation ...Nef mediated downregulation of CD28 cell surface expression / positive regulation of inflammatory response to antigenic stimulus / regulatory T cell differentiation / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / CD4-positive, alpha-beta T cell proliferation / positive regulation of isotype switching to IgG isotypes / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / CD28 co-stimulation / CD28 dependent Vav1 pathway / CD28 dependent PI3K/Akt signaling / positive regulation of interleukin-10 production / 液性免疫 / 免疫シナプス / positive regulation of interleukin-4 production / positive regulation of viral genome replication / coreceptor activity / positive regulation of T cell proliferation / T cell costimulation / positive regulation of interleukin-2 production / T細胞 / positive regulation of mitotic nuclear division / positive regulation of translation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cytokine production / apoptotic signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / T cell receptor signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protease binding / transcription by RNA polymerase II / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / 細胞膜 / positive regulation of transcription by RNA polymerase II / identical protein binding / 細胞膜 / 細胞質基質 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: 2.7 Å | ||||||
データ登録者 | Evans, E.J. / Esnouf, R.M. / Manso-Sancho, R. / Gilbert, R.J.C. / James, J.R. / Sorensen, P. / Stuart, D.I. / Davis, S.J. | ||||||
引用 | ジャーナル: Nat Immunol / 年: 2005 タイトル: Crystal structure of a soluble CD28-Fab complex. 著者: Edward J Evans / Robert M Esnouf / Raquel Manso-Sancho / Robert J C Gilbert / John R James / Chao Yu / Janet A Fennelly / Cheryl Vowles / Thomas Hanke / Björn Walse / Thomas Hünig / Poul ...著者: Edward J Evans / Robert M Esnouf / Raquel Manso-Sancho / Robert J C Gilbert / John R James / Chao Yu / Janet A Fennelly / Cheryl Vowles / Thomas Hanke / Björn Walse / Thomas Hünig / Poul Sørensen / David I Stuart / Simon J Davis / 要旨: Naive T cell activation requires signaling by the T cell receptor and by nonclonotypic cell surface receptors. The most important costimulatory protein is the monovalent homodimer CD28, which ...Naive T cell activation requires signaling by the T cell receptor and by nonclonotypic cell surface receptors. The most important costimulatory protein is the monovalent homodimer CD28, which interacts with CD80 and CD86 expressed on antigen-presenting cells. Here we present the crystal structure of a soluble form of CD28 in complex with the Fab fragment of a mitogenic antibody. Structural comparisons redefine the evolutionary relationships of CD28-related proteins, antigen receptors and adhesion molecules and account for the distinct ligand-binding and stoichiometric properties of CD28 and the related, inhibitory homodimer CTLA-4. Cryo-electron microscopy-based comparisons of complexes of CD28 with mitogenic and nonmitogenic antibodies place new constraints on models of antibody-induced receptor triggering. This work completes the initial structural characterization of the CD28-CTLA-4-CD80-CD86 signaling system. | ||||||
履歴 |
|
-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
---|
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 1yjd.cif.gz | 119.3 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb1yjd.ent.gz | 95.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1yjd.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/yj/1yjd ftp://data.pdbj.org/pub/pdb/validation_reports/yj/1yjd | HTTPS FTP |
---|
-関連構造データ
-リンク
-集合体
登録構造単位 |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
単位格子 |
| ||||||||
詳細 | The second part of the biological assembly is generated by the two fold axis: 1-x, y, 1-z. |
-要素
#1: 抗体 | 分子量: 23388.822 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) | ||
---|---|---|---|
#2: 抗体 | 分子量: 24108.939 Da / 分子数: 1 / Fragment: IgV and IgC1 domains / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) | ||
#3: タンパク質 | 分子量: 15784.077 Da / 分子数: 1 / Fragment: Extracellular region / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CD28 / プラスミド: PEE14 発現宿主: Cricetulus griseus (モンゴルキヌゲネズミ) 株 (発現宿主): CHO Lec3.2.8.1 / 参照: UniProt: P10747 | ||
#4: 糖 | #5: 水 | ChemComp-HOH / | |
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 3 |
---|
-試料調製
結晶 | マシュー密度: 2.95 Å3/Da / 溶媒含有率: 58.4 % |
---|---|
結晶化 | 温度: 294 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 5.9 詳細: PEG 3350, magnesium formate, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-データ収集
回折 | 平均測定温度: 100 K |
---|---|
放射光源 | 由来: シンクロトロン / サイト: ESRF / ビームライン: ID13 / 波長: 1.008 Å |
検出器 | タイプ: MARRESEARCH / 検出器: CCD / 日付: 2002年12月2日 |
放射 | モノクロメーター: Si 111 CHANNEL / 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: 1.008 Å / 相対比: 1 |
反射 | 解像度: 2.7→25 Å / Num. all: 18408 / Num. obs: 17413 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.15 |
反射 シェル | 解像度: 2.7→2.8 Å / % possible all: 97.4 |
-解析
ソフトウェア |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 構造決定の手法: 分子置換 / 解像度: 2.7→25 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / σ(F): 0 / 立体化学のターゲット値: Engh & Huber
| |||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 80 Å2
| |||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.7→25 Å
| |||||||||||||||||||||||||
LS精密化 シェル | 解像度: 2.7→2.78 Å /
|