+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7orh | ||||||
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タイトル | Ternary complex of 14-3-3 sigma, p27pT198 phosphopeptide, and WQ178 | ||||||
要素 |
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キーワード | SIGNALING PROTEIN / protein-peptide complex small-molecule | ||||||
機能・相同性 | 機能・相同性情報 cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of epithelial cell proliferation involved in prostate gland development / regulation of cell cycle G1/S phase transition / negative regulation of phosphorylation / regulation of exit from mitosis ...cyclin-dependent protein kinase activating kinase regulator activity / regulation of lens fiber cell differentiation / negative regulation of cardiac muscle tissue regeneration / negative regulation of cyclin-dependent protein kinase activity / autophagic cell death / FOXO-mediated transcription of cell cycle genes / negative regulation of epithelial cell proliferation involved in prostate gland development / regulation of cell cycle G1/S phase transition / negative regulation of phosphorylation / regulation of exit from mitosis / epithelial cell proliferation involved in prostate gland development / negative regulation of epithelial cell apoptotic process / negative regulation of cyclin-dependent protein serine/threonine kinase activity / ubiquitin ligase activator activity / cyclin-dependent protein serine/threonine kinase inhibitor activity / RHO GTPases activate CIT / nuclear export / AKT phosphorylates targets in the cytosol / epithelial cell apoptotic process / cellular response to antibiotic / Cul4A-RING E3 ubiquitin ligase complex / molecular function inhibitor activity / negative regulation of kinase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / cellular response to lithium ion / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / p53-Dependent G1 DNA Damage Response / protein kinase inhibitor activity / PTK6 Regulates Cell Cycle / regulation of cell-cell adhesion / regulation of G1/S transition of mitotic cell cycle / Constitutive Signaling by AKT1 E17K in Cancer / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / negative regulation of vascular associated smooth muscle cell proliferation / inner ear development / Regulation of localization of FOXO transcription factors / cellular response to organic cyclic compound / keratinocyte proliferation / negative regulation of mitotic cell cycle / phosphoserine residue binding / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / response to amino acid / establishment of skin barrier / negative regulation of protein localization to plasma membrane / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / response to cadmium ion / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / response to glucose / Cyclin E associated events during G1/S transition / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / Cyclin A:Cdk2-associated events at S phase entry / positive regulation of protein localization / RHO GTPases activate PKNs / Notch signaling pathway / positive regulation of microtubule polymerization / protein sequestering activity / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / protein kinase A signaling / FLT3 Signaling / protein export from nucleus / Hsp70 protein binding / negative regulation of innate immune response / regulation of cell migration / positive regulation of cell adhesion / cyclin binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / positive regulation of DNA replication / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / sensory perception of sound / negative regulation of protein kinase activity / placenta development / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / negative regulation of cell growth / SCF(Skp2)-mediated degradation of p27/p21 / response to peptide hormone / positive regulation of protein catabolic process / G1/S transition of mitotic cell cycle / intrinsic apoptotic signaling pathway in response to DNA damage / Cyclin D associated events in G1 / cellular senescence / protein localization / response to estradiol / regulation of protein localization / heart development / protein-folding chaperone binding / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
手法 | X線回折 / 分子置換 / 解像度: 1.8 Å | ||||||
データ登録者 | Centorrino, F. / Wu, Q. / Ottmann, C. | ||||||
資金援助 | European Union, 1件
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引用 | ジャーナル: To Be Published タイトル: A crystallography-based study of fragment extensions into the 14-3-3 binding groove 著者: Centorrino, F. / Wu, Q. / Cossar, P. / Brunsveld, L. / Ottmann, C. | ||||||
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 | 7orh.cif.gz | 135 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7orh.ent.gz | 85.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7orh.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 | 7orh_validation.pdf.gz | 1011.1 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7orh_full_validation.pdf.gz | 1014.3 KB | 表示 | |
XML形式データ | 7orh_validation.xml.gz | 14.6 KB | 表示 | |
CIF形式データ | 7orh_validation.cif.gz | 21.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/or/7orh ftp://data.pdbj.org/pub/pdb/validation_reports/or/7orh | HTTPS FTP |
-関連構造データ
関連構造データ | 7opwC 7oq7C 7oq8C 7oq9C 7oqaC 7oqgC 7oqjC 7oqsC 7oquC 7oqwC 7or3C 7or5C 7or7C 7or8C 7orgC 7orsC 7ortC 4jc3S S: 精密化の開始モデル 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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単位格子 |
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Components on special symmetry positions |
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-要素
-タンパク質 / タンパク質・ペプチド , 2種, 2分子 AP
#1: タンパク質 | 分子量: 28226.518 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SFN, HME1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P31947 |
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#2: タンパク質・ペプチド | 分子量: 1522.712 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) Homo sapiens (ヒト) / 参照: UniProt: P46527 |
-非ポリマー , 4種, 299分子
#3: 化合物 | #4: 化合物 | #5: 化合物 | ChemComp-CL / | #6: 水 | ChemComp-HOH / | |
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-詳細
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: 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: 2.4 Å3/Da / 溶媒含有率: 48.84 % |
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結晶化 | 温度: 277.15 K / 手法: 蒸気拡散法, シッティングドロップ法 詳細: 0.095 M Hepes pH7.3, 26%PEG 400, 0.19 M CaCl2, and 5 % Glycerol |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: SEALED TUBE / タイプ: RIGAKU MICROMAX-003 / 波長: 1.54187 Å |
検出器 | タイプ: DECTRIS PILATUS 200K / 検出器: PIXEL / 日付: 2021年2月22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: 1.54187 Å / 相対比: 1 |
反射 | 解像度: 1.8→41.53 Å / Num. obs: 26790 / % possible obs: 99.7 % / 冗長度: 6.1 % / Biso Wilson estimate: 13.12 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.4 |
反射 シェル | 解像度: 1.8→1.83 Å / 冗長度: 4.9 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1291 / CC1/2: 0.874 / % possible all: 95.8 |
-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: 4jc3 解像度: 1.8→41.53 Å / SU ML: 0.1816 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 20.0666 / 立体化学のターゲット値: GeoStd + Monomer Library
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溶媒の処理 | 減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | Biso mean: 17.11 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: LAST / 解像度: 1.8→41.53 Å
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拘束条件 |
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LS精密化 シェル |
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