+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5ol0 | ||||||
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タイトル | Structure of Leishmania infantum Silent Information Regulator 2 related protein 1 (LiSIR2rp1) in complex with acetylated p53 peptide | ||||||
要素 |
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キーワード | HYDROLASE (加水分解酵素) / NAD-dependent histone deacetylase | ||||||
機能・相同性 | 機能・相同性情報 protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase 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 ...protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase 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 / negative regulation of DNA replication / ER overload response / B cell lineage commitment / 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 / glycosyltransferase activity / 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 / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / cellular response to actinomycin D / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / response to X-ray / ヘイフリック限界 / chromosome organization / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / NAD+ binding / 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 / type II interferon-mediated signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of stem cell proliferation / core promoter sequence-specific DNA binding / negative regulation of fibroblast proliferation / cardiac muscle cell apoptotic process 類似検索 - 分子機能 | ||||||
生物種 | Leishmania infantum (幼児リーシュマニア) Homo sapiens (ヒト) | ||||||
手法 | X線回折 / シンクロトロン / 分子置換 / 解像度: 1.99 Å | ||||||
データ登録者 | Ronin, C. / Ciesielski, F. / Ciapetti, P. | ||||||
資金援助 | フランス, 1件
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引用 | ジャーナル: PLoS ONE / 年: 2018 タイトル: The crystal structure of the Leishmania infantum Silent Information Regulator 2 related protein 1: Implications to protein function and drug design. 著者: Ronin, C. / Costa, D.M. / Tavares, J. / Faria, J. / Ciesielski, F. / Ciapetti, P. / Smith, T.K. / MacDougall, J. / Cordeiro-da-Silva, A. / Pemberton, I.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 | 5ol0.cif.gz | 130.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5ol0.ent.gz | 99.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 5ol0.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/ol/5ol0 ftp://data.pdbj.org/pub/pdb/validation_reports/ol/5ol0 | HTTPS FTP |
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-関連構造データ
関連構造データ | 3gltS 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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1 |
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2 |
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単位格子 |
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-要素
#1: タンパク質 | 分子量: 35373.152 Da / 分子数: 2 / 由来タイプ: 組換発現 詳細: Compared to Uniprot sequence Q8I6E4, region P253-E300 was deleted from expressed sequence 由来: (組換発現) Leishmania infantum (幼児リーシュマニア) 遺伝子: SIR2RP1, LINJ_26_0200 / 発現宿主: Escherichia coli (大腸菌) 参照: UniProt: Q8I6E4, NAD+-protein-arginine ADP-ribosyltransferase #2: タンパク質・ペプチド | 分子量: 2139.521 Da / 分子数: 2 / Fragment: UNP residues 372-389 / 由来タイプ: 合成 / 詳細: ACETYLATED P53 LYS-382 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P04637 #3: 化合物 | #4: 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: 2.06 Å3/Da / 溶媒含有率: 40.24 % |
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結晶化 | 温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.5 / 詳細: 100mM Na Hepes pH7.5; 25% PEG2000 MME |
-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: SOLEIL / ビームライン: PROXIMA 1 / 波長: 0.978 Å |
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2016年2月24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: 0.978 Å / 相対比: 1 |
反射 | 解像度: 1.99→46.56 Å / Num. obs: 38331 / % possible obs: 98.8 % / 冗長度: 3.3 % / Rsym value: 0.047 / Net I/σ(I): 15.43 |
反射 シェル | 解像度: 1.99→2.11 Å / 冗長度: 3.14 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 5913 / Rsym value: 0.506 / % possible all: 95.4 |
-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: 3glt 解像度: 1.99→46.56 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.913 / SU ML: 0.131 / 交差検証法: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.164 / 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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溶媒の処理 | イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 41.374 Å2
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精密化ステップ | サイクル: 1 / 解像度: 1.99→46.56 Å
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拘束条件 |
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