+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1hu8 | ||||||
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タイトル | CRYSTAL STRUCTURE OF THE MOUSE P53 CORE DNA-BINDING DOMAIN AT 2.7A RESOLUTION | ||||||
要素 | CELLULAR TUMOR ANTIGEN P53 | ||||||
キーワード | DNA BINDING PROTEIN / p53 / tumor suppressor / DNA binding | ||||||
機能・相同性 | 機能・相同性情報 Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Regulation of TP53 Expression / Regulation of TP53 Activity through Acetylation / Transcriptional activation of cell cycle inhibitor p21 / Regulation of TP53 Activity through Association with Co-factors / RUNX3 regulates CDKN1A transcription / regulation of thymocyte apoptotic process / PI5P Regulates TP53 Acetylation / DNA Damage/Telomere Stress Induced Senescence / Stabilization of p53 ...Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Regulation of TP53 Expression / Regulation of TP53 Activity through Acetylation / Transcriptional activation of cell cycle inhibitor p21 / Regulation of TP53 Activity through Association with Co-factors / RUNX3 regulates CDKN1A transcription / regulation of thymocyte apoptotic process / PI5P Regulates TP53 Acetylation / DNA Damage/Telomere Stress Induced Senescence / Stabilization of p53 / Regulation of TP53 Activity through Methylation / G2/M DNA damage checkpoint / Regulation of TP53 Degradation / Oncogene Induced Senescence / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M Checkpoints / Ovarian tumor domain proteases / PKR-mediated signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / The role of GTSE1 in G2/M progression after G2 checkpoint / regulation of cellular senescence / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / Ub-specific processing proteases / negative regulation of DNA biosynthetic process / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing 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 / embryo development ending in birth or egg hatching / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / positive regulation of leukocyte migration / regulation of DNA damage response, signal transduction by p53 class mediator / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / mitochondrial DNA repair / T cell lineage commitment / negative regulation of DNA replication / ER overload response / B cell lineage commitment / positive regulation of cardiac muscle cell apoptotic process / thymocyte apoptotic process / cardiac septum morphogenesis / positive regulation of execution phase of apoptosis / entrainment of circadian clock by photoperiod / necroptotic process / positive regulation of release of cytochrome c from mitochondria / TFIID-class transcription factor complex binding / rRNA transcription / mitophagy / negative regulation of telomere maintenance via telomerase / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of mitotic cell cycle / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuroblast proliferation / cellular response to UV-C / : / hematopoietic stem cell differentiation / negative regulation of reactive oxygen species metabolic process / chromosome organization / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / T cell proliferation involved in immune response / glial cell proliferation / embryonic organ development / positive regulation of RNA polymerase II transcription preinitiation complex assembly / cellular response to glucose starvation / cellular response to actinomycin D / somitogenesis / positive regulation of cell cycle / regulation of neuron apoptotic process / type II interferon-mediated signaling pathway / response to UV / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / gastrulation 類似検索 - 分子機能 | ||||||
生物種 | 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 | Zhao, K. / Chai, X. / Johnston, K. / Clements, A. / Marmorstein, R. | ||||||
引用 | ジャーナル: J.Biol.Chem. / 年: 2001 タイトル: Crystal structure of the mouse p53 core DNA-binding domain at 2.7 A resolution. 著者: Zhao, K. / Chai, X. / Johnston, K. / Clements, A. / Marmorstein, R. | ||||||
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 | 1hu8.cif.gz | 122.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1hu8.ent.gz | 96.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1hu8.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 | 1hu8_validation.pdf.gz | 438.3 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1hu8_full_validation.pdf.gz | 466.7 KB | 表示 | |
XML形式データ | 1hu8_validation.xml.gz | 25.8 KB | 表示 | |
CIF形式データ | 1hu8_validation.cif.gz | 34.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/hu/1hu8 ftp://data.pdbj.org/pub/pdb/validation_reports/hu/1hu8 | HTTPS FTP |
-関連構造データ
関連構造データ | 1tsrS S: 精密化の開始モデル |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 20928.838 Da / 分子数: 3 / 断片: RESIDUES 99-284 / 変異: Y199A / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 株: DH5A / 遺伝子: P53 / プラスミド: PRSET / 生物種 (発現宿主): Escherichia coli / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: P02340 #2: 化合物 | #3: 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: 3.07 Å3/Da / 溶媒含有率: 57 % | ||||||||||||||||||||||||||||||||||||
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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: 7.5 詳細: PEG 4000, KCl and MgCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS | ||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 180 K |
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放射光源 | 由来: シンクロトロン / サイト: CHESS / ビームライン: A1 / 波長: 1.0801 Å |
検出器 | タイプ: ADSC QUANTUM 4 / 検出器: CCD / 日付: 2000年6月7日 / 詳細: mirrors |
放射 | モノクロメーター: YALE MIRRORS / 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: 1.0801 Å / 相対比: 1 |
反射 | 解像度: 2.7→100 Å / Num. all: 121009 / Num. obs: 22733 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / 冗長度: 5.3 % / Biso Wilson estimate: 71.7 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 9.6 |
反射 シェル | 解像度: 2.7→2.85 Å / 冗長度: 4.8 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3242 / Rsym value: 0.186 / % possible all: 99.5 |
反射 | *PLUS 最低解像度: 10 Å / Num. measured all: 121009 |
反射 シェル | *PLUS % possible obs: 98.7 % / Rmerge(I) obs: 0.189 |
-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: PDB ENTRY 1TSR 解像度: 2.7→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high rms absF: 1546899.25 / Isotropic thermal model: Isotropic / 交差検証法: THROUGHOUT / σ(F): 2 / σ(I): 2 / 立体化学のターゲット値: Engh & Huber
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原子変位パラメータ | Biso mean: 63.5 Å2
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Refine analyze |
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精密化ステップ | サイクル: LAST / 解像度: 2.7→10 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.7→2.79 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 10
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Xplor file |
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ソフトウェア | *PLUS 名称: CNS / バージョン: 0.9 / 分類: refinement | ||||||||||||||||||||||||||||||||||||
精密化 | *PLUS 最高解像度: 2.7 Å / 最低解像度: 10 Å / σ(F): 2 / % reflection Rfree: 9.9 % / Rfactor obs: 0.239 | ||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor Rfree: 0.449 / Rfactor Rwork: 0.383 |