+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8j8n | ||||||
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タイトル | Structure of p53 DNA-binding domain and ZNF568 KRAB domain complex | ||||||
要素 |
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キーワード | PROTEIN BINDING / p53 DBD / ZNF 568 KRAB / p53-dependent glycosis / mitochondrial respiration | ||||||
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 / regulation of fibroblast apoptotic process / 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 ...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 / regulation of fibroblast apoptotic process / 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 / 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 / circadian behavior / mRNA transcription / bone marrow development / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / RUNX3 regulates CDKN1A transcription / 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 / negative regulation of neuroblast proliferation / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / positive regulation of cardiac muscle cell apoptotic process / ER overload response / negative regulation of DNA replication / 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 / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / entrainment of circadian clock by photoperiod / Association of TriC/CCT with target proteins during biosynthesis / PI5P Regulates TP53 Acetylation / positive regulation of execution phase of apoptosis / necroptotic process / Zygotic genome activation (ZGA) / positive regulation of release of cytochrome c from mitochondria / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / rRNA transcription / TFIID-class transcription factor complex binding / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / response to X-ray / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / replicative senescence / mitophagy / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / neuroblast proliferation / cellular response to UV-C / hematopoietic stem cell differentiation / chromosome organization / negative regulation of reactive oxygen species metabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / T cell proliferation involved in immune response / hematopoietic progenitor cell differentiation / glial cell proliferation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / embryonic organ development / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / cellular response to actinomycin D / cellular response to glucose starvation / type II interferon-mediated signaling pathway / core promoter sequence-specific DNA binding / negative regulation of stem cell proliferation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / cardiac muscle cell apoptotic process / tumor necrosis factor-mediated signaling pathway / mitotic G1 DNA damage checkpoint signaling / Regulation of TP53 Activity through Acetylation / response to salt stress / 14-3-3 protein binding / viral process 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 9.02 Å | ||||||
データ登録者 | Han, C.W. | ||||||
資金援助 | 韓国, 1件
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引用 | ジャーナル: To Be Published タイトル: Structure of p53 DNA-binding domain and ZNF568 KRAB domain complex 著者: Han, C.W. | ||||||
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 | 8j8n.cif.gz | 206.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8j8n.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 8j8n.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 | 8j8n_validation.pdf.gz | 1.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8j8n_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | 8j8n_validation.xml.gz | 55.4 KB | 表示 | |
CIF形式データ | 8j8n_validation.cif.gz | 77.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j8/8j8n ftp://data.pdbj.org/pub/pdb/validation_reports/j8/8j8n | HTTPS FTP |
-関連構造データ
関連構造データ | 36075MC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 13940.639 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: ZNF568 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: C9JLX5 #2: タンパク質 | 分子量: 22658.805 Da / 分子数: 4 / Fragment: DNA binding domain / 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 (大腸菌) / 参照: UniProt: P04637 #3: 化合物 | ChemComp-ZN / 研究の焦点であるリガンドがあるか | Y | |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: The complex of p53 DNA binding domain and ZNF568 KRAB domain タイプ: COMPLEX / Entity ID: #1-#2 / 由来: RECOMBINANT |
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分子量 | 値: 0.126 MDa / 実験値: YES |
由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Escherichia coli (大腸菌) |
緩衝液 | pH: 7.8 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: 22mA / グリッドの材料: GOLD / グリッドのサイズ: 200 divisions/in. / グリッドのタイプ: Quantifoil R2/2 |
急速凍結 | 凍結剤: NITROGEN |
-電子顕微鏡撮影
顕微鏡 | モデル: TFS GLACIOS |
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電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: DARK FIELD / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 2000 nm |
撮影 | 電子線照射量: 40 e/Å2 フィルム・検出器のモデル: FEI FALCON III (4k x 4k) |
-解析
ソフトウェア |
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CTF補正 | 詳細: ZNF568 KRAB used PDB ID 7W5Q p53 DBD used PDB ID 7DVD タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 9.02 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 76698 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
精密化 | 立体化学のターゲット値: CDL v1.2 | ||||||||||||||||||||||||
拘束条件 |
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