+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-23738 | |||||||||
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タイトル | Cryo-EM structure of MLL1-NCP (H3K4M) complex, mode01 | |||||||||
マップデータ | Mode01 | |||||||||
試料 |
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キーワード | MLL1-NCP / H3K4 methylation / TRANSFERASE / TRANSFERASE-DNA BINDING PROTEIN-DNA complex | |||||||||
機能・相同性 | 機能・相同性情報 protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / T-helper 2 cell differentiation / MLL3/4 complex / regulation of short-term neuronal synaptic plasticity ...protein-cysteine methyltransferase activity / response to potassium ion / [histone H3]-lysine4 N-methyltransferase / histone H3K4 monomethyltransferase activity / unmethylated CpG binding / histone H3K4 trimethyltransferase activity / negative regulation of DNA methylation-dependent heterochromatin formation / T-helper 2 cell differentiation / MLL3/4 complex / regulation of short-term neuronal synaptic plasticity / Set1C/COMPASS complex / MLL1/2 complex / definitive hemopoiesis / ATAC complex / NSL complex / histone H3K4 methyltransferase activity / Cardiogenesis / embryonic hemopoiesis / exploration behavior / anterior/posterior pattern specification / regulation of tubulin deacetylation / histone methyltransferase complex / Formation of WDR5-containing histone-modifying complexes / regulation of cell division / minor groove of adenine-thymine-rich DNA binding / membrane depolarization / regulation of embryonic development / hemopoiesis / MLL1 complex / histone acetyltransferase complex / negative regulation of fibroblast proliferation / homeostasis of number of cells within a tissue / positive regulation of gluconeogenesis / spleen development / lysine-acetylated histone binding / cellular response to transforming growth factor beta stimulus / methylated histone binding / transcription initiation-coupled chromatin remodeling / 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの / post-embryonic development / skeletal system development / gluconeogenesis / Deactivation of the beta-catenin transactivating complex / Transcriptional regulation of granulopoiesis / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / circadian regulation of gene expression / PKMTs methylate histone lysines / visual learning / protein modification process / euchromatin / RMTs methylate histone arginines / mitotic spindle / Activation of anterior HOX genes in hindbrain development during early embryogenesis / beta-catenin binding / response to estrogen / structural constituent of chromatin / nucleosome / nucleosome assembly / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / HATs acetylate histones / histone binding / fibroblast proliferation / protein-containing complex assembly / methylation / transcription cis-regulatory region binding / regulation of cell cycle / protein heterodimerization activity / chromatin binding / positive regulation of cell population proliferation / DNA damage response / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / regulation of DNA-templated transcription / nucleolus / apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Xenopus laevis (アフリカツメガエル) / synthetic construct (人工物) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 | |||||||||
データ登録者 | Park SH / Ayoub A | |||||||||
資金援助 | 米国, 2件
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引用 | ジャーナル: Biochemistry / 年: 2022 タイトル: Regulation of MLL1 Methyltransferase Activity in Two Distinct Nucleosome Binding Modes. 著者: Alex Ayoub / Sang Ho Park / Young-Tae Lee / Uhn-Soo Cho / Yali Dou / 要旨: Cryo-EM structures of the KMT2A/MLL1 core complex bound on nucleosome core particles (NCPs) suggest unusual rotational dynamics of the MLL1 complex approaching its physiological substrate. However, ...Cryo-EM structures of the KMT2A/MLL1 core complex bound on nucleosome core particles (NCPs) suggest unusual rotational dynamics of the MLL1 complex approaching its physiological substrate. However, the functional implication of such dynamics remains unclear. Here, we show that the MLL1 core complex also shows high rotational dynamics bound on the NCP carrying the catalytically inert histone H3 lysine 4 to methionine (K4M) mutation. There are two major binding modes of the MLL1 complex on the NCP. Importantly, disruption of only one of the binding modes compromised the overall MLL1 activity in an NCP-specific manner. We propose that the MLL1 core complex probably exists in an equilibrium of poised and active binding modes. The high rotational dynamics of the MLL1 complex on the NCP is a feature that can be exploited for loci-specific regulation of H3K4 methylation in higher eukaryotes. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_23738.map.gz | 11.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-23738-v30.xml emd-23738.xml | 23.1 KB 23.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_23738_fsc.xml | 16.2 KB | 表示 | FSCデータファイル |
画像 | emd_23738.png | 55.8 KB | ||
Filedesc metadata | emd-23738.cif.gz | 7.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-23738 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23738 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_23738_validation.pdf.gz | 379.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_23738_full_validation.pdf.gz | 379.2 KB | 表示 | |
XML形式データ | emd_23738_validation.xml.gz | 12.8 KB | 表示 | |
CIF形式データ | emd_23738_validation.cif.gz | 17.2 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23738 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23738 | 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_23738.map.gz / 形式: CCP4 / 大きさ: 163.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Mode01 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
+全体 : MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nu...
+超分子 #1: MLL1 in complex with RbBP5, WDR5, SET1, and ASH2L bound to the nu...
+超分子 #2: RbBP5, WDR5, SET1, and ASH2L
+超分子 #3: nucleosome
+分子 #1: Retinoblastoma-binding protein 5
+分子 #2: WD repeat-containing protein 5
+分子 #3: Histone-lysine N-methyltransferase 2A
+分子 #4: Set1/Ash2 histone methyltransferase complex subunit ASH2
+分子 #5: Histone H3
+分子 #6: Histone H4
+分子 #7: Histone H2A
+分子 #8: Histone H2B 1.1
+分子 #9: DNA (145-MER)
+分子 #10: DNA (145-MER)
-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 / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV |
-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 K2 SUMMIT (4k x 4k) 平均電子線量: 53.4 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: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | プロトコル: RIGID BODY FIT |
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得られたモデル | PDB-7mbm: |