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万見- EMDB-43197: Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome -
+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-43197 | |||||||||
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タイトル | Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome | |||||||||
マップデータ | main map | |||||||||
試料 |
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キーワード | nucleosome / pioneer transcription factors / DNA binding proteins / transcription / chromatin / NUCLEAR PROTEIN / NUCLEAR PROTEIN-DNA complex | |||||||||
機能・相同性 | 機能・相同性情報 alveolar secondary septum development / respiratory basal cell differentiation / prostate gland stromal morphogenesis / positive regulation of dopaminergic neuron differentiation / atrial septum secundum morphogenesis / atrioventricular valve formation / transdifferentiation / embryonic heart tube anterior/posterior pattern specification / mesenchymal-epithelial cell signaling involved in prostate gland development / Formation of lateral plate mesoderm ...alveolar secondary septum development / respiratory basal cell differentiation / prostate gland stromal morphogenesis / positive regulation of dopaminergic neuron differentiation / atrial septum secundum morphogenesis / atrioventricular valve formation / transdifferentiation / embryonic heart tube anterior/posterior pattern specification / mesenchymal-epithelial cell signaling involved in prostate gland development / Formation of lateral plate mesoderm / anatomical structure formation involved in morphogenesis / positive regulation of cell-cell adhesion mediated by cadherin / intestinal epithelial cell differentiation / epithelial cell maturation involved in prostate gland development / cardiac right ventricle morphogenesis / atrioventricular node development / co-SMAD binding / cell growth involved in cardiac muscle cell development / atrial septum morphogenesis / cardiac muscle tissue regeneration / endocardial cushion development / neuron fate specification / Transcriptional regulation of testis differentiation / cardiac ventricle morphogenesis / Physiological factors / atrial septum primum morphogenesis / secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development / lung epithelial cell differentiation / embryonic foregut morphogenesis / atrioventricular canal development / YAP1- and WWTR1 (TAZ)-stimulated gene expression / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / dorsal/ventral neural tube patterning / endoderm development / Formation of definitive endoderm / prostate gland epithelium morphogenesis / Formation of axial mesoderm / dopaminergic neuron differentiation / positive regulation of BMP signaling pathway / positive regulation of smoothened signaling pathway / negative regulation of epithelial to mesenchymal transition / hormone metabolic process / response to vitamin A / regulation of cardiac muscle cell contraction / aortic valve morphogenesis / Cardiogenesis / positive regulation of intracellular estrogen receptor signaling pathway / ventricular septum development / negative regulation of cardiac muscle cell apoptotic process / DNA-binding transcription activator activity / smoothened signaling pathway / epithelial tube branching involved in lung morphogenesis / cell fate commitment / detection of maltose stimulus / maltose transport complex / NFAT protein binding / heart looping / carbohydrate transport / protein localization to CENP-A containing chromatin / microvillus / CENP-A containing nucleosome / negative regulation of apoptotic signaling pathway / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / negative regulation of tumor necrosis factor-mediated signaling pathway / positive regulation of vascular endothelial growth factor production / anatomical structure morphogenesis / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / Packaging Of Telomere Ends / lipoxygenase pathway / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / hepoxilin biosynthetic process / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / response to mechanical stimulus / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / Notch signaling pathway / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / ATP-binding cassette (ABC) transporter complex / DNA methylation / positive regulation of mitotic cell cycle / negative regulation of autophagy 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / synthetic construct (人工物) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.48 Å | |||||||||
データ登録者 | Zhou BR / Bai Y | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Mol.Cell / 年: 2024 タイトル: Cryo-EM structure of FoxA1 and GATA4 in complex with ALBN1 nucleosome 著者: Zhou BR / Bai Y | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_43197.map.gz | 96.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-43197-v30.xml emd-43197.xml | 23.1 KB 23.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_43197_fsc.xml | 11.1 KB | 表示 | FSCデータファイル |
画像 | emd_43197.png | 109.5 KB | ||
Filedesc metadata | emd-43197.cif.gz | 7.4 KB | ||
その他 | emd_43197_half_map_1.map.gz emd_43197_half_map_2.map.gz | 3.7 MB 3.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-43197 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43197 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_43197_validation.pdf.gz | 495.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_43197_full_validation.pdf.gz | 494.9 KB | 表示 | |
XML形式データ | emd_43197_validation.xml.gz | 17.9 KB | 表示 | |
CIF形式データ | emd_43197_validation.cif.gz | 23.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43197 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-43197 | HTTPS FTP |
-関連構造データ
関連構造データ | 8vg1MC M: このマップから作成された原子モデル 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
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_43197.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | main map | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.056 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-ハーフマップ: half B
ファイル | emd_43197_half_map_1.map | ||||||||||||
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注釈 | half B | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: half A
ファイル | emd_43197_half_map_2.map | ||||||||||||
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注釈 | half A | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : FoxA1 and GATA4 in complx with 186bp ALBN1 nucleosome
+超分子 #1: FoxA1 and GATA4 in complx with 186bp ALBN1 nucleosome
+分子 #1: Histone H3.1
+分子 #2: Histone H4
+分子 #3: Histone H2A type 1-B/E
+分子 #4: Histone H2B type 1-J
+分子 #7: Hepatocyte nuclear factor 3-alpha
+分子 #8: Maltose/maltodextrin-binding periplasmic protein,Transcription fa...
+分子 #5: DNA (171-MER)
+分子 #6: DNA (171-MER)
+分子 #9: ZINC ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | TFS KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 1.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: OTHER / 撮影モード: OTHER / 最大 デフォーカス(公称値): 1.8 µm / 最小 デフォーカス(公称値): 0.8 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |