+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1czy | ||||||
---|---|---|---|---|---|---|---|
タイトル | CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE TRAF DOMAIN OF HUMAN TRAF2 AND AN LMP1 BINDING PEPTIDE | ||||||
要素 |
| ||||||
キーワード | APOPTOSIS / BETA SANDWICH / PROTEIN-PEPTIDE COMPLEX / SIGNALING PROTEIN | ||||||
機能・相同性 | 機能・相同性情報 CD40 receptor binding / tumor necrosis factor receptor superfamily complex / symbiont-mediated activation of host NF-kappaB cascade / sphingolipid binding / IRE1-TRAF2-ASK1 complex / Defective RIPK1-mediated regulated necrosis / TRAF2-GSTP1 complex / tumor necrosis factor binding / CD40 signaling pathway / Regulation by c-FLIP ...CD40 receptor binding / tumor necrosis factor receptor superfamily complex / symbiont-mediated activation of host NF-kappaB cascade / sphingolipid binding / IRE1-TRAF2-ASK1 complex / Defective RIPK1-mediated regulated necrosis / TRAF2-GSTP1 complex / tumor necrosis factor binding / CD40 signaling pathway / Regulation by c-FLIP / CASP8 activity is inhibited / Dimerization of procaspase-8 / interleukin-17-mediated signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / negative regulation of glial cell apoptotic process / TNF signaling / Caspase activation via Death Receptors in the presence of ligand / programmed necrotic cell death / CD40 receptor complex / regulation of immunoglobulin production / signal transduction involved in regulation of gene expression / positive regulation of tumor necrosis factor-mediated signaling pathway / mitogen-activated protein kinase kinase kinase binding / tumor necrosis factor receptor binding / thioesterase binding / mRNA stabilization / positive regulation of extrinsic apoptotic signaling pathway / vesicle membrane / TNFR1-induced proapoptotic signaling / non-canonical NF-kappaB signal transduction / RIPK1-mediated regulated necrosis / TRAF6 mediated IRF7 activation / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / TRAF6 mediated NF-kB activation / protein K63-linked ubiquitination / regulation of JNK cascade / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / host cell membrane / cellular response to nitric oxide / regulation of protein-containing complex assembly / protein autoubiquitination / signaling adaptor activity / ubiquitin ligase complex / positive regulation of JUN kinase activity / tumor necrosis factor-mediated signaling pathway / response to endoplasmic reticulum stress / positive regulation of interleukin-2 production / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / TNFR2 non-canonical NF-kB pathway / positive regulation of DNA-binding transcription factor activity / Regulation of TNFR1 signaling / RING-type E3 ubiquitin transferase / protein catabolic process / Regulation of necroptotic cell death / positive regulation of T cell cytokine production / cytoplasmic side of plasma membrane / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / cell cortex / protein-macromolecule adaptor activity / protein-containing complex assembly / protein phosphatase binding / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / Ub-specific processing proteases / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / membrane raft / innate immune response / virus-mediated perturbation of host defense response / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / host cell plasma membrane / enzyme binding / signal transduction / zinc ion binding / nucleoplasm / identical protein binding / membrane / cytosol / cytoplasm 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 / 解像度: 2 Å | ||||||
データ登録者 | Ye, H. / Park, Y.C. / Kreishman, M. / Kieff, E. / Wu, H. | ||||||
引用 | ジャーナル: Mol.Cell / 年: 1999 タイトル: The structural basis for the recognition of diverse receptor sequences by TRAF2. 著者: Ye, H. / Park, Y.C. / Kreishman, M. / Kieff, E. / Wu, H. #1: ジャーナル: Nature / 年: 1999 タイトル: Structural Basis for Self-Association and Receptor Recognition of Human Traf2 著者: Park, Y.C. / Burkitt, V. / Villa, A.R. / Tong, L. / Wu, H. | ||||||
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 | 1czy.cif.gz | 117.4 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb1czy.ent.gz | 90.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1czy.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
文書・要旨 | 1czy_validation.pdf.gz | 387.5 KB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 1czy_full_validation.pdf.gz | 396.8 KB | 表示 | |
XML形式データ | 1czy_validation.xml.gz | 12.8 KB | 表示 | |
CIF形式データ | 1czy_validation.cif.gz | 20.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/cz/1czy ftp://data.pdbj.org/pub/pdb/validation_reports/cz/1czy | 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 |
|
-要素
#1: タンパク質 | 分子量: 19032.953 Da / 分子数: 3 / 断片: TRAF DOMAIN / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / プラスミド: PET24D / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q12933 #2: タンパク質・ペプチド | 分子量: 799.783 Da / 分子数: 2 / 断片: TRAF2-BINDING REGION / 由来タイプ: 合成 詳細: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE NATURALLY OCCURS IN HUMANS (HOMO SAPIENS) 参照: UniProt: P03230 #3: 水 | ChemComp-HOH / | 構成要素の詳細 | THE DEPOSITED TRAF2-RECEPTOR PEPTIDE COMPLEX CONTAINS 3 TRAF2 PER ASYMMETRIC UNIT, ONE OF WHICH ...THE DEPOSITED TRAF2-RECEPTOR PEPTIDE COMPLEX CONTAINS 3 TRAF2 PER ASYMMETRIC | Has protein modification | Y | |
---|
-実験情報
-実験
実験 | 手法: X線回折 / 使用した結晶の数: 1 |
---|
-試料調製
結晶 | マシュー密度: 2.45 Å3/Da / 溶媒含有率: 49.89 % | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
結晶化 | 温度: 293 K / 手法: 蒸気拡散法 / pH: 6 詳細: PEG4K, MES BUFFER, pH 6.00, VAPOR DIFFUSION, temperature 20K | |||||||||||||||
結晶化 | *PLUS 手法: unknown | |||||||||||||||
溶液の組成 | *PLUS
|
-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: NSLS / ビームライン: X4A / 波長: 1.018 |
検出器 | タイプ: RIGAKU RAXIS IV / 検出器: IMAGE PLATE |
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: 1.018 Å / 相対比: 1 |
反射 | *PLUS 最高解像度: 2 Å / % possible obs: 99.7 % / Rmerge(I) obs: 0.055 |
反射 シェル | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.15 |
-解析
ソフトウェア |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 解像度: 2→20 Å
| ||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2→20 Å
|