+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4xr8 | |||||||||
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タイトル | Crystal structure of the HPV16 E6/E6AP/p53 ternary complex at 2.25 A resolution | |||||||||
要素 |
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キーワード | VIRAL PROTEIN/ ANTITUMOR PROTEIN (ウイルス性) / Human papillomavirus 16 / E6 oncoprotein / Ubiquitin-Ligase E6AP / tumor suppressor p53 (P53遺伝子) / p53 degradation / viral protein-antitumor protein (ウイルス性) / VIRAL PROTEIN- ANTITUMOR PROTEIN complex (ウイルス性) | |||||||||
機能・相同性 | 機能・相同性情報 symbiont-mediated suppression of host transcription / regulation of proteolysis / activation of GTPase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator ...symbiont-mediated suppression of host transcription / regulation of proteolysis / activation of GTPase activity / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / 転写 (生物学) / bone marrow development / circadian behavior / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of neuroblast proliferation / negative regulation of glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / mitochondrial DNA repair / T cell lineage commitment / detection of maltose stimulus / maltose binding / maltose transport complex / negative regulation of DNA replication / ER overload response / maltose transport / B cell lineage commitment / maltodextrin transmembrane transport / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / rRNA transcription / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / マイトファジー / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / carbohydrate transmembrane transporter activity / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / cellular response to actinomycin D / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / carbohydrate transport / ヘイフリック限界 / chromosome organization / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / gastrulation / cellular response to UV-C / response to inorganic substance / hematopoietic stem cell differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of RNA polymerase II transcription preinitiation complex assembly / negative regulation of reactive oxygen species metabolic process / MDM2/MDM4 family protein binding / embryonic organ development / glial cell proliferation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / cellular response to glucose starvation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis 類似検索 - 分子機能 | |||||||||
生物種 | Escherichia coli (大腸菌) HOMO SAPIENS (ヒト) Homo sapiens (ヒト) Human papillomavirus type 16 (パピローマウイルス) | |||||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 2.25 Å | |||||||||
データ登録者 | Martinez-Zapien, D. / Ruiz, F.X. / Mitschler, A. / Podjarny, A. / Trave, G. / Zanier, K. | |||||||||
引用 | ジャーナル: Nature / 年: 2016 タイトル: Structure of the E6/E6AP/p53 complex required for HPV-mediated degradation of p53. 著者: Martinez-Zapien, D. / Ruiz, F.X. / Poirson, J. / Mitschler, A. / Ramirez, J. / Forster, A. / Cousido-Siah, A. / Masson, M. / Pol, S.V. / Podjarny, A. / Trave, G. / Zanier, K. | |||||||||
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 | 4xr8.cif.gz | 306.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4xr8.ent.gz | 246.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4xr8.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/xr/4xr8 ftp://data.pdbj.org/pub/pdb/validation_reports/xr/4xr8 | 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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1 |
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2 |
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単位格子 |
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-要素
-タンパク質 , 3種, 6分子 ABCDFH
#1: タンパク質 | 分子量: 41803.258 Da / 分子数: 2 / 変異: D83A,K84A,K240A,E360A,D364A,K363A / 由来タイプ: 組換発現 由来: (組換発現) Escherichia coli (大腸菌), (組換発現) HOMO SAPIENS (ヒト) 株: K12 / 遺伝子: malE, b4034, JW3994 / 発現宿主: Escherichia coli K-12 (大腸菌) / 参照: UniProt: P0AEX9 #2: タンパク質 | 分子量: 22448.531 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: TP53, P53 / 発現宿主: Escherichia coli K-12 (大腸菌) / 参照: UniProt: P04637 #3: タンパク質 | 分子量: 18301.107 Da / 分子数: 2 / 変異: C80S,C97S,C111S,C140S / 由来タイプ: 組換発現 由来: (組換発現) Human papillomavirus type 16 (パピローマウイルス) 遺伝子: E6 / 発現宿主: Escherichia coli K-12 (大腸菌) / 参照: UniProt: P03126 |
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-糖 , 1種, 2分子
#4: 多糖 |
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-非ポリマー , 4種, 365分子
#5: 化合物 | ChemComp-PEG / #6: 化合物 | ChemComp-ZN / #7: 化合物 | ChemComp-EDO / | #8: 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: 2.48 Å3/Da / 溶媒含有率: 50.34 % |
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結晶化 | 温度: 290 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5 / 詳細: 7.5 % PEG 20K, 0.05 M MES pH 6.5 |
-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: SLS / ビームライン: X06DA / 波長: 1 Å |
検出器 | タイプ: DECTRIS PILATUS 2M / 検出器: PIXEL / 日付: 2013年10月10日 |
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: 2.25→50 Å / Num. obs: 77282 / % possible obs: 98.56 % / 冗長度: 3.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.52 |
反射 シェル | 解像度: 2.25→2.33 Å / 冗長度: 3.1 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 1.99 / % possible all: 89.64 |
-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: 4GIZ, 1TUP 解像度: 2.25→49.635 Å / SU ML: 0.33 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 27.63 / 立体化学のターゲット値: ML
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.25→49.635 Å
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拘束条件 |
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LS精密化 シェル |
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