+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2bip | ||||||
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タイトル | human p53 core domain mutant M133L-H168R-V203A-N239Y-R249S-N268D | ||||||
要素 | CELLULAR TUMOR ANTIGEN P53P53遺伝子 | ||||||
キーワード | DNA BINDING PROTEIN (DNA結合タンパク質) / ACTIVATOR / ANTI-ONCOGENE (がん抑制遺伝子) / APOPTOSIS (アポトーシス) / DISEASE MUTATION / DNA-BINDING / DNA-BINDING PROTEIN (DNA結合タンパク質) / LI-FRAUMENI SYNDROME / NUCLEAR PROTEIN / P53 DNA-BINDING DOMAIN / PHOSPHORYLATION (リン酸化) / POLYMORPHISM / SECOND-SITE SUPPRESSOR MUTATION / SUPERSTABLE MUTANT / TRANSCRIPTION REGULATION / TUMOR SUPPRESSOR (がん抑制遺伝子) / TRANSFERASE (転移酵素) / ACETYLATION (アセチル化) / GLYCOPROTEIN METAL-BINDING / ZINC (亜鉛) | ||||||
機能・相同性 | 機能・相同性情報 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 ...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 / histone deacetylase regulator activity / regulation of mitochondrial membrane permeability involved in apoptotic process / 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 glial cell proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / positive regulation of execution phase of apoptosis / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / positive regulation of cardiac muscle cell apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / T cell proliferation involved in immune response / cardiac septum morphogenesis / entrainment of circadian clock by photoperiod / 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 / SUMOylation of transcription factors / negative regulation of telomere maintenance via telomerase / general transcription initiation factor binding / intrinsic apoptotic signaling pathway by p53 class mediator / Transcriptional Regulation by VENTX / response to X-ray / DNA damage response, signal transduction by p53 class mediator / ヘイフリック限界 / chromosome organization / neuroblast proliferation / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to UV-C / : / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / glial cell proliferation / embryonic organ development / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / cellular response to glucose starvation / cellular response to actinomycin D / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / type II interferon-mediated signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / gastrulation / negative regulation of fibroblast proliferation / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / transcription initiation-coupled chromatin remodeling / 14-3-3 protein binding / mitotic G1 DNA damage checkpoint signaling / Regulation of TP53 Activity through Acetylation / response to salt stress 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: 1.8 Å | ||||||
データ登録者 | Joerger, A.C. / Fersht, A.R. | ||||||
引用 | ジャーナル: J.Biol.Chem. / 年: 2005 タイトル: Structures of P53 Cancer Mutants and Mechanism of Rescue by Second-Site Suppressor Mutations 著者: Joerger, A.C. / Ang, H.C. / Veprintsev, D.B. / Blair, C.M. / Fersht, A.R. #1: ジャーナル: J.Biol.Chem. / 年: 2004 タイトル: Crystal Structure of a Superstable Mutant of Human P53 Core Domain: Insights Into the Mechanism of Rescuing Oncogenic Mutations 著者: Joerger, A.C. / Allen, M.D. / Fersht, A.R. #2: ジャーナル: Science / 年: 1994 タイトル: Crystal Structure of a P53 Tumor Suppressor-DNA Complex: Understanding Tumorigenic Mutations 著者: Cho, Y. / Gorina, S. / Jeffrey, P.D. / Pavletich, N.P. | ||||||
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 | 2bip.cif.gz | 55.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2bip.ent.gz | 38.4 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2bip.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/bi/2bip ftp://data.pdbj.org/pub/pdb/validation_reports/bi/2bip | 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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単位格子 |
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-要素
#1: タンパク質 | 分子量: 24539.775 Da / 分子数: 1 / 断片: DNA-BINDING (CORE) DOMAIN, RESIDUES 94-312 / 変異: YES / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / 発現宿主: ESCHERICHIA COLI (大腸菌) / 参照: UniProt: P04637 |
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#2: 化合物 | ChemComp-ZN / |
#3: 水 | ChemComp-HOH / |
構成要素の詳細 | FUNCTION: TUMOR SUPPRESSOR IN MANY TUMOR TYPES ENGINEERED MUTATIONS IN CHAIN A MET 133 TO LEU, HIS ...FUNCTION: TUMOR SUPPRESSOR |
-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: 2.23 Å3/Da / 溶媒含有率: 44.45 % |
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-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: SRS / ビームライン: PX14.1 / 波長: 1.488 |
検出器 | タイプ: ADSC CCD / 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: 1.488 Å / 相対比: 1 |
反射 | 解像度: 1.8→39.3 Å / Num. obs: 19672 / % possible obs: 98.4 % / 冗長度: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.4 |
反射 シェル | 解像度: 1.8→1.9 Å / 冗長度: 3 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.9 / % possible all: 97.2 |
-解析
ソフトウェア | 名称: CNS / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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精密化 | 構造決定の手法: 分子置換 開始モデル: PDB ENTRY 1UOL 解像度: 1.8→39.3 Å / 交差検証法: THROUGHOUT
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精密化ステップ | サイクル: LAST / 解像度: 1.8→39.3 Å
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拘束条件 |
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