+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-28631 | |||||||||
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タイトル | CX3CR1 nucleosome bound PU.1 and C/EBPa | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | nucleosome / transcription factor / transcription / CHROMATIN BINDING PROTEIN-DNA complex / DNA BINDING PROTEIN / TRANSCRIPTION-DNA complex | |||||||||
機能・相同性 | 機能・相同性情報 positive regulation of myeloid dendritic cell chemotaxis / anatomical structure regression / follicular B cell differentiation / positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / pro-T cell differentiation / negative regulation of neutrophil degranulation / germinal center B cell differentiation / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity ...positive regulation of myeloid dendritic cell chemotaxis / anatomical structure regression / follicular B cell differentiation / positive regulation of antifungal innate immune response / regulation of myeloid progenitor cell differentiation / pro-T cell differentiation / negative regulation of neutrophil degranulation / germinal center B cell differentiation / myeloid leukocyte differentiation / positive regulation of microglial cell mediated cytotoxicity / granulocyte differentiation / lymphocyte differentiation / apoptotic process involved in blood vessel morphogenesis / endothelial to hematopoietic transition / negative regulation of adipose tissue development / pericyte cell differentiation / immature B cell differentiation / negative regulation of MHC class II biosynthetic process / lymphoid progenitor cell differentiation / myeloid dendritic cell differentiation / vasculature development / regulation of DNA-binding transcription factor activity / oncogene-induced cell senescence / negative regulation of protein localization to chromatin / positive regulation of p38MAPK cascade / positive regulation of B cell differentiation / NFAT protein binding / somatic stem cell population maintenance / macrophage differentiation / negative regulation of megakaryocyte differentiation / heterochromatin organization / protein localization to CENP-A containing chromatin / cis-regulatory region sequence-specific DNA binding / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / epigenetic regulation of gene expression / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / nucleosomal DNA binding / lipopolysaccharide-mediated signaling pathway / transcription initiation-coupled chromatin remodeling / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / protein sequestering activity / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / erythrocyte differentiation / DNA methylation / transforming growth factor beta receptor signaling pathway / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / G2/M DNA damage checkpoint / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / PKMTs methylate histone lysines / Meiotic recombination / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / antimicrobial humoral immune response mediated by antimicrobial peptide / UCH proteinases / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / HATs acetylate histones / Processing of DNA double-strand break ends 類似検索 - 分子機能 | |||||||||
生物種 | Mus musculus (ハツカネズミ) / Homo sapiens (ヒト) / Escherichia coli (大腸菌) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.1 Å | |||||||||
データ登録者 | Lian T / Guan R / Bai Y | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2024 タイトル: Structural mechanism of synergistic targeting of the CX3CR1 nucleosome by PU.1 and C/EBPα. 著者: Tengfei Lian / Ruifang Guan / Bing-Rui Zhou / Yawen Bai / 要旨: Pioneer transcription factors are vital for cell fate changes. PU.1 and C/EBPα work together to regulate hematopoietic stem cell differentiation. However, how they recognize in vivo nucleosomal DNA ...Pioneer transcription factors are vital for cell fate changes. PU.1 and C/EBPα work together to regulate hematopoietic stem cell differentiation. However, how they recognize in vivo nucleosomal DNA targets remains elusive. Here we report the structures of the nucleosome containing the mouse genomic CX3CR1 enhancer DNA and its complexes with PU.1 alone and with both PU.1 and the C/EBPα DNA binding domain. Our structures reveal that PU.1 binds the DNA motif at the exit linker, shifting 17 bp of DNA into the core region through interactions with H2A, unwrapping ~20 bp of nucleosomal DNA. C/EBPα binding, aided by PU.1's repositioning, unwraps ~25 bp of entry DNA. The PU.1 Q218H mutation, linked to acute myeloid leukemia, disrupts PU.1-H2A interactions. PU.1 and C/EBPα jointly displace linker histone H1 and open the H1-condensed nucleosome array. Our study unveils how two pioneer factors can work cooperatively to open closed chromatin by altering DNA positioning in the nucleosome. | |||||||||
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_28631.map.gz | 34.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-28631-v30.xml emd-28631.xml | 21.3 KB 21.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_28631.png | 60.3 KB | ||
Filedesc metadata | emd-28631.cif.gz | 6.6 KB | ||
その他 | emd_28631_half_map_1.map.gz emd_28631_half_map_2.map.gz | 40.9 MB 40.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-28631 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28631 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_28631_validation.pdf.gz | 829.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_28631_full_validation.pdf.gz | 829.1 KB | 表示 | |
XML形式データ | emd_28631_validation.xml.gz | 11.8 KB | 表示 | |
CIF形式データ | emd_28631_validation.cif.gz | 13.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28631 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28631 | HTTPS FTP |
-関連構造データ
-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_28631.map.gz / 形式: CCP4 / 大きさ: 52.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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: #2
ファイル | emd_28631_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_28631_half_map_2.map | ||||||||||||
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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 : nucleosome complexed with PU.1 and C/EBPa
全体 | 名称: nucleosome complexed with PU.1 and C/EBPa |
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要素 |
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-超分子 #1: nucleosome complexed with PU.1 and C/EBPa
超分子 | 名称: nucleosome complexed with PU.1 and C/EBPa / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
-分子 #1: DNA (167-MER)
分子 | 名称: DNA (167-MER) / タイプ: dna / ID: 1 / コピー数: 1 / 分類: DNA |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 51.538973 KDa |
配列 | 文字列: (DT)(DA)(DG)(DA)(DA)(DA)(DA)(DA)(DT)(DA) (DG)(DG)(DA)(DA)(DC)(DC)(DC)(DC)(DA)(DC) (DA)(DT)(DG)(DC)(DC)(DC)(DT)(DG)(DT) (DG)(DT)(DC)(DT)(DG)(DC)(DA)(DA)(DG)(DT) (DA) (DC)(DA)(DG)(DA)(DA) ...文字列: (DT)(DA)(DG)(DA)(DA)(DA)(DA)(DA)(DT)(DA) (DG)(DG)(DA)(DA)(DC)(DC)(DC)(DC)(DA)(DC) (DA)(DT)(DG)(DC)(DC)(DC)(DT)(DG)(DT) (DG)(DT)(DC)(DT)(DG)(DC)(DA)(DA)(DG)(DT) (DA) (DC)(DA)(DG)(DA)(DA)(DC)(DT)(DA) (DG)(DC)(DC)(DA)(DG)(DA)(DC)(DA)(DG)(DA) (DC)(DT) (DG)(DA)(DC)(DC)(DT)(DA)(DT) (DT)(DT)(DT)(DT)(DG)(DT)(DG)(DA)(DG)(DG) (DG)(DG)(DA) (DA)(DT)(DC)(DG)(DG)(DG) (DA)(DA)(DG)(DT)(DA)(DT)(DC)(DC)(DA)(DT) (DT)(DG)(DC)(DT) (DA)(DA)(DG)(DA)(DC) (DT)(DC)(DA)(DG)(DC)(DA)(DA)(DT)(DG)(DC) (DT)(DG)(DC)(DA)(DA) (DC)(DT)(DC)(DT) (DC)(DA)(DG)(DC)(DA)(DA)(DC)(DC)(DA)(DG) (DC)(DT)(DG)(DA)(DA)(DG) (DA)(DT)(DC) (DA)(DG)(DC)(DA)(DG)(DC)(DC)(DG)(DA)(DG) (DA)(DG)(DG)(DC)(DC)(DC)(DT) (DG)(DC) (DA)(DC)(DC)(DT)(DA) |
-分子 #2: DNA (167-MER)
分子 | 名称: DNA (167-MER) / タイプ: dna / ID: 2 / コピー数: 1 / 分類: DNA |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 51.558816 KDa |
配列 | 文字列: (DT)(DA)(DG)(DG)(DT)(DG)(DC)(DA)(DG)(DG) (DG)(DC)(DC)(DT)(DC)(DT)(DC)(DG)(DG)(DC) (DT)(DG)(DC)(DT)(DG)(DA)(DT)(DC)(DT) (DT)(DC)(DA)(DG)(DC)(DT)(DG)(DG)(DT)(DT) (DG) (DC)(DT)(DG)(DA)(DG) ...文字列: (DT)(DA)(DG)(DG)(DT)(DG)(DC)(DA)(DG)(DG) (DG)(DC)(DC)(DT)(DC)(DT)(DC)(DG)(DG)(DC) (DT)(DG)(DC)(DT)(DG)(DA)(DT)(DC)(DT) (DT)(DC)(DA)(DG)(DC)(DT)(DG)(DG)(DT)(DT) (DG) (DC)(DT)(DG)(DA)(DG)(DA)(DG)(DT) (DT)(DG)(DC)(DA)(DG)(DC)(DA)(DT)(DT)(DG) (DC)(DT) (DG)(DA)(DG)(DT)(DC)(DT)(DT) (DA)(DG)(DC)(DA)(DA)(DT)(DG)(DG)(DA)(DT) (DA)(DC)(DT) (DT)(DC)(DC)(DC)(DG)(DA) (DT)(DT)(DC)(DC)(DC)(DC)(DT)(DC)(DA)(DC) (DA)(DA)(DA)(DA) (DA)(DT)(DA)(DG)(DG) (DT)(DC)(DA)(DG)(DT)(DC)(DT)(DG)(DT)(DC) (DT)(DG)(DG)(DC)(DT) (DA)(DG)(DT)(DT) (DC)(DT)(DG)(DT)(DA)(DC)(DT)(DT)(DG)(DC) (DA)(DG)(DA)(DC)(DA)(DC) (DA)(DG)(DG) (DG)(DC)(DA)(DT)(DG)(DT)(DG)(DG)(DG)(DG) (DT)(DT)(DC)(DC)(DT)(DA)(DT) (DT)(DT) (DT)(DT)(DC)(DT)(DA) |
-分子 #3: Histone H3.1
分子 | 名称: Histone H3.1 / タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 15.437167 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVALR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEACEA YLVGLFEDTN LCAIHAKRVT IMPKDIQLAR RIRGERA UniProtKB: Histone H3.1 |
-分子 #4: Histone H4
分子 | 名称: Histone H4 / タイプ: protein_or_peptide / ID: 4 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 11.394426 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG UniProtKB: Histone H4 |
-分子 #5: Histone H2A type 2-C
分子 | 名称: Histone H2A type 2-C / タイプ: protein_or_peptide / ID: 5 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 14.019467 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MSGRGKQGGK ARAKAKSRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YMAAVLEYLT AEILELAGNA ARDNKKCRII PRHLQLAIR NDEELNKLLG KVTIAQGGVL PNIQAVLLPK KTESHKAKSK UniProtKB: Histone H2A type 2-C |
-分子 #6: Histone H2B type 2-E
分子 | 名称: Histone H2B type 2-E / タイプ: protein_or_peptide / ID: 6 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 13.951239 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSSK UniProtKB: Histone H2B type 2-E |
-分子 #7: ScFv
分子 | 名称: ScFv / タイプ: protein_or_peptide / ID: 7 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: Escherichia coli (大腸菌) |
分子量 | 理論値: 29.030146 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MKSSHHHHHH ENLYFQSNAM EVQLQQSGPE LVEPGTSVKM PCKASGYTFT SYTIQWVKQT PRQGLEWIGY IYPYNAGTKY NEKFKGKAT LTSDKSSSTV YMELSSLTSE DSAVYYCARK SSRLRSTLDY WGQGTSVTVS SGGGGSGGGG SGGGGSMDIK M TQSPSSMH ...文字列: MKSSHHHHHH ENLYFQSNAM EVQLQQSGPE LVEPGTSVKM PCKASGYTFT SYTIQWVKQT PRQGLEWIGY IYPYNAGTKY NEKFKGKAT LTSDKSSSTV YMELSSLTSE DSAVYYCARK SSRLRSTLDY WGQGTSVTVS SGGGGSGGGG SGGGGSMDIK M TQSPSSMH ASLGERVTIT CKASQDIRSY LSWYQQKPWK SPKTLIYYAT SLADGVPSRF SGSGSGQDFS LTINNLESDD TA TYYCLQH GESPYTFGSG TKLEIKRA |
-分子 #8: Transcription factor PU.1
分子 | 名称: Transcription factor PU.1 / タイプ: protein_or_peptide / ID: 8 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
分子量 | 理論値: 32.865844 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MGSSHHHHHH SSGMLQACKM EGFSLTAPPS DDLVTYDSEL YQRPMHDYYS FVGSDGESHS DHYWDFSAHH VHNNEFENFP ENHFTELQS VQPPQLQQLY RHMELEQMHV LDTPMVPPHT GLSHQVSYMP RMCFPYQTLS PAHQQSSDEE EGERQSPPLE V SDGEADGL ...文字列: MGSSHHHHHH SSGMLQACKM EGFSLTAPPS DDLVTYDSEL YQRPMHDYYS FVGSDGESHS DHYWDFSAHH VHNNEFENFP ENHFTELQS VQPPQLQQLY RHMELEQMHV LDTPMVPPHT GLSHQVSYMP RMCFPYQTLS PAHQQSSDEE EGERQSPPLE V SDGEADGL EPGPGLLHGE TGSKKKIRLY QFLLDLLRSG DMKDSIWWVD KDKGTFQFSS KHKEALAHRW GIQKCNRKKM TY QKMARAL RNYGKTGEVK KVKKKLTYQF SGEVLGRGGL AERRLPPH UniProtKB: Transcription factor PU.1 |
-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: 7.1 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN 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: 53.8 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: SPOT SCAN / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 1.0 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: NONE |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 4.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 15710 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |