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基本情報
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タイトル | Cryo-EM structure of human cohesin-CTCF-DNA complex | ||||||||||||
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![]() | Cohesin / NIPBL / CTCF / DNA / chromosome folding / topologically associating domain / chromatin loops / DNA loop extrusion / sister chromatid cohesion / complex / ATPase / HEAT repeat protein / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||||||||
機能・相同性 | ![]() eye morphogenesis / external genitalia morphogenesis / gallbladder development / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / mitotic cohesin loading / response to DNA damage checkpoint signaling / regulation of hair cycle / chromatin loop anchoring activity ...eye morphogenesis / external genitalia morphogenesis / gallbladder development / SMC loading complex / Scc2-Scc4 cohesin loading complex / ear morphogenesis / mitotic cohesin loading / response to DNA damage checkpoint signaling / regulation of hair cycle / chromatin loop anchoring activity / negative regulation of mitotic metaphase/anaphase transition / cohesin loader activity / chromatin insulator sequence binding / positive regulation of sister chromatid cohesion / meiotic cohesin complex / Cohesin Loading onto Chromatin / maintenance of mitotic sister chromatid cohesion / Establishment of Sister Chromatid Cohesion / forelimb morphogenesis / embryonic viscerocranium morphogenesis / establishment of meiotic sister chromatid cohesion / mitotic cohesin complex / cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / uterus morphogenesis / regulation of centromeric sister chromatid cohesion / negative regulation of glial cell apoptotic process / establishment of protein localization to chromatin / regulation of developmental growth / genomic imprinting / embryonic digestive tract morphogenesis / replication-born double-strand break repair via sister chromatid exchange / cellular response to X-ray / lateral element / integrator complex / positive regulation of neuron migration / mediator complex binding / chromo shadow domain binding / establishment of mitotic sister chromatid cohesion / protein localization to chromosome, centromeric region / positive regulation of multicellular organism growth / metanephros development / chromatin looping / positive regulation of ossification / digestive tract development / reciprocal meiotic recombination / embryonic forelimb morphogenesis / sister chromatid cohesion / lncRNA binding / face morphogenesis / negative regulation of interleukin-1 beta production / microtubule motor activity / negative regulation of gene expression via chromosomal CpG island methylation / mitotic sister chromatid cohesion / stem cell population maintenance / dynein complex binding / mitotic spindle pole / fat cell differentiation / beta-tubulin binding / outflow tract morphogenesis / regulation of DNA replication / mitotic sister chromatid segregation / somatic stem cell population maintenance / positive regulation of interleukin-10 production / regulation of embryonic development / negative regulation of tumor necrosis factor production / chromosome, centromeric region / mitotic spindle assembly / developmental growth / SUMOylation of DNA damage response and repair proteins / heart morphogenesis / condensed chromosome / epigenetic regulation of gene expression / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / condensed nuclear chromosome / meiotic cell cycle / male germ cell nucleus / transcription coregulator binding / chromosome segregation / promoter-specific chromatin binding / sensory perception of sound / response to radiation / brain development / kinetochore / cognition / DNA-binding transcription repressor activity, RNA polymerase II-specific / spindle pole / histone deacetylase binding / nuclear matrix / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Separation of Sister Chromatids / transcription corepressor activity / protein localization / sequence-specific double-stranded DNA binding / double-strand break repair / chromosome / mitotic cell cycle / midbody 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.5 Å | ||||||||||||
![]() | Shi ZB / Bai XC | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: CTCF and R-loops are boundaries of cohesin-mediated DNA looping. 著者: Hongshan Zhang / Zhubing Shi / Edward J Banigan / Yoori Kim / Hongtao Yu / Xiao-Chen Bai / Ilya J Finkelstein / ![]() ![]() 要旨: Cohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional (3D) genome organization. Cohesin extrudes DNA loops that are anchored by CTCF in a polar orientation. Here, ...Cohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional (3D) genome organization. Cohesin extrudes DNA loops that are anchored by CTCF in a polar orientation. Here, we present direct evidence that CTCF binding polarity controls cohesin-mediated DNA looping. Using single-molecule imaging, we demonstrate that a critical N-terminal motif of CTCF blocks cohesin translocation and DNA looping. The cryo-EM structure of the cohesin-CTCF complex reveals that this CTCF motif ahead of zinc fingers can only reach its binding site on the STAG1 cohesin subunit when the N terminus of CTCF faces cohesin. Remarkably, a C-terminally oriented CTCF accelerates DNA compaction by cohesin. DNA-bound Cas9 and Cas12a ribonucleoproteins are also polar cohesin barriers, indicating that stalling may be intrinsic to cohesin itself. Finally, we show that RNA-DNA hybrids (R-loops) block cohesin-mediated DNA compaction in vitro and are enriched with cohesin subunits in vivo, likely forming TAD boundaries. | ||||||||||||
履歴 |
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構造の表示
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マップデータ | ![]() | 104.5 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 29.9 KB 29.9 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 12.8 KB | 表示 | ![]() |
画像 | ![]() | 63.1 KB | ||
Filedesc metadata | ![]() | 11.1 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 402.9 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 402.5 KB | 表示 | |
XML形式データ | ![]() | 12.9 KB | 表示 | |
CIF形式データ | ![]() | 17.6 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7w1mMC 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 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.44 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
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試料の構成要素
+全体 : Human cohesin-NIPBL-CTCF-DNA complex
+超分子 #1: Human cohesin-NIPBL-CTCF-DNA complex
+超分子 #2: Human cohesin-NIPBL-CTCF
+超分子 #3: DNA
+分子 #1: Structural maintenance of chromosomes protein 1A
+分子 #2: Structural maintenance of chromosomes protein 3
+分子 #3: Double-strand-break repair protein rad21 homolog
+分子 #4: Cohesin subunit SA-1
+分子 #5: Nipped-B-like protein
+分子 #8: Transcriptional repressor CTCF
+分子 #6: DNA (118-MER)
+分子 #7: DNA (118-MER)
+分子 #9: ADENOSINE-5'-DIPHOSPHATE
+分子 #10: BERYLLIUM TRIFLUORIDE ION
+分子 #11: 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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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.5 |
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K |
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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) / 撮影したグリッド数: 1 / 平均電子線量: 60.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
-原子モデル構築 1
初期モデル |
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精密化 | 空間: REAL / プロトコル: RIGID BODY FIT | ||||||||||||
得られたモデル | ![]() PDB-7w1m: |