+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4a63 | ||||||
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タイトル | Crystal structure of the p73-ASPP2 complex at 2.6A resolution | ||||||
要素 |
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キーワード | CELL CYCLE (細胞周期) / TP53BP2 / TUMOUR SUPPRESSOR (がん抑制遺伝子) / ANKYRINS / APOPTOSIS REGULATORY PROTEINS (アポトーシス) | ||||||
機能・相同性 | 機能・相同性情報 positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / positive regulation of oligodendrocyte differentiation / 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 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release ...positive regulation of lung ciliated cell differentiation / negative regulation of cardiac muscle cell proliferation / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / Regulation of TP53 Activity through Association with Co-factors / positive regulation of execution phase of apoptosis / positive regulation of oligodendrocyte differentiation / 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 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of cell cycle / negative regulation of neuron differentiation / NF-kappaB binding / DNAミスマッチ修復 / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / MDM2/MDM4 family protein binding / response to organonitrogen compound / regulation of mitotic cell cycle / transcription corepressor binding / kidney development / protein tetramerization / SH3 domain binding / intrinsic apoptotic signaling pathway in response to DNA damage / p53 binding / 細胞結合 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / 遺伝子発現の調節 / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of MAPK cascade / transcription cis-regulatory region binding / regulation of cell cycle / DNA-binding transcription factor activity, RNA polymerase II-specific / response to xenobiotic stimulus / 細胞周期 / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / DNA damage response / クロマチン / regulation of transcription by RNA polymerase II / protein kinase binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / ゴルジ体 / シグナル伝達 / positive regulation of transcription by RNA polymerase II / 核質 / identical protein binding / metal ion binding / 細胞核 / 細胞質基質 / 細胞質 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: 2.27 Å | ||||||
データ登録者 | Canning, P. / Sharpe, T. / Krojer, T. / Savitsky, P. / Cooper, C.D.O. / Salah, E. / Keates, T. / Muniz, J. / Vollmar, M. / von Delft, F. ...Canning, P. / Sharpe, T. / Krojer, T. / Savitsky, P. / Cooper, C.D.O. / Salah, E. / Keates, T. / Muniz, J. / Vollmar, M. / von Delft, F. / Weigelt, J. / Arrowsmith, C. / Bountra, C. / Edwards, A. / Bullock, A.N. | ||||||
引用 | ジャーナル: J.Mol.Biol. / 年: 2012 タイトル: Structural Basis for Aspp2 Recognition by the Tumor Suppressor P73. 著者: Canning, P. / von Delft, F. / Bullock, A.N. | ||||||
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 | 4a63.cif.gz | 479.4 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4a63.ent.gz | 390 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4a63.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/a6/4a63 ftp://data.pdbj.org/pub/pdb/validation_reports/a6/4a63 | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
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単位格子 |
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非結晶学的対称性 (NCS) | NCS oper:
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-要素
#1: タンパク質 | 分子量: 23342.561 Da / 分子数: 6 / 断片: DNA-BINDING DOMAIN, RESIDUES 1-208 / 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) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): R3 PRARE2 / 参照: UniProt: O15350 #2: タンパク質 | 分子量: 26951.475 Da / 分子数: 6 / 断片: ANKYRIN AND SH3 DOMAINS, RESIDUES 892-1128 / 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) / 株 (発現宿主): BL21(DE3) / Variant (発現宿主): R3 / 参照: UniProt: Q13625 #3: 化合物 | ChemComp-ZN / #4: 化合物 | ChemComp-ACT / #5: 水 | ChemComp-HOH / | 非ポリマーの詳細 | ACETATE (ACT): PRESENT IN CRYSTALLIZ | |
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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: 3.32 Å3/Da / 溶媒含有率: 63.03 % / 解説: NONE |
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結晶化 | 詳細: 1.00M NA/KPO4, 0.1M ACETATE PH 4.5 |
-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: Diamond / ビームライン: I03 / 波長: 0.9763 |
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2011年7月4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: 0.9763 Å / 相対比: 1 |
反射 | 解像度: 2.6→88.72 Å / Num. obs: 111026 / % possible obs: 97.4 % / Observed criterion σ(I): 2 / 冗長度: 3.7 % / Biso Wilson estimate: 43.51 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.4 |
反射 シェル | 解像度: 2.65→2.79 Å / 冗長度: 3.8 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.1 / % possible all: 95.6 |
-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 ENTRIES 2XWC AND 1YCS CHAIN B 解像度: 2.27→85.05 Å / Cor.coef. Fo:Fc: 0.7815 / Cor.coef. Fo:Fc free: 0.908 / SU R Cruickshank DPI: 0.217 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.212 / SU Rfree Blow DPI: 0.181 / SU Rfree Cruickshank DPI: 0.184 詳細: INITIAL REFINEMENT WITH REFMAC BUSTER 2.1 PHENIX.XTRIAGE. THE ANALYSES OF THE PATTERSON FUNCTION REVEALS A SIGNIFICANT OFF-ORIGIN PEAK THAT IS 47.52 PERCENT OF THE ORIGIN PEAK, INDICATING ...詳細: INITIAL REFINEMENT WITH REFMAC BUSTER 2.1 PHENIX.XTRIAGE. THE ANALYSES OF THE PATTERSON FUNCTION REVEALS A SIGNIFICANT OFF-ORIGIN PEAK THAT IS 47.52 PERCENT OF THE ORIGIN PEAK, INDICATING PSEUDO TRANSLATIONAL SYMMETRY. IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=19288. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0 NUMBER TREATED BY BAD NON-BONDED CONTACTS=6.
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原子変位パラメータ | Biso mean: 51.05 Å2
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Refine analyze | Luzzati coordinate error obs: 0.305 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 2.27→85.05 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.27→2.33 Å / Total num. of bins used: 20
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