+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-31042 | ||||||||||||
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タイトル | Yeast Set2 bound to wild-type nucleosome | ||||||||||||
マップデータ | |||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 PKMTs methylate histone lysines / negative regulation of antisense RNA transcription / ascospore formation / negative regulation of reciprocal meiotic recombination / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / DNA-templated transcription elongation / histone H3K36 methyltransferase activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of DNA-templated DNA replication initiation ...PKMTs methylate histone lysines / negative regulation of antisense RNA transcription / ascospore formation / negative regulation of reciprocal meiotic recombination / [histone H3]-lysine36 N-trimethyltransferase / histone H3K36 trimethyltransferase activity / DNA-templated transcription elongation / histone H3K36 methyltransferase activity / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of DNA-templated DNA replication initiation / DNA-templated transcription termination / structural constituent of chromatin / nucleosome / nucleosome assembly / methylation / protein heterodimerization activity / regulation of DNA-templated transcription / chromatin / DNA binding / nucleoplasm / nucleus / cytosol 類似検索 - 分子機能 | ||||||||||||
生物種 | Xenopus laevis (アフリカツメガエル) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.3 Å | ||||||||||||
データ登録者 | Jing H / Liu Y | ||||||||||||
資金援助 | 中国, 3件
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引用 | ジャーナル: Cell Discov / 年: 2021 タイトル: Cryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations. 著者: Yingying Liu / Yanjun Zhang / Han Xue / Mi Cao / Guohui Bai / Zongkai Mu / Yanli Yao / Shuyang Sun / Dong Fang / Jing Huang / 要旨: Substitution of lysine 36 with methionine in histone H3.3 (H3.3K36M) is an oncogenic mutation that inhibits SETD2-mediated histone H3K36 tri-methylation in tumors. To investigate how the oncohistone ...Substitution of lysine 36 with methionine in histone H3.3 (H3.3K36M) is an oncogenic mutation that inhibits SETD2-mediated histone H3K36 tri-methylation in tumors. To investigate how the oncohistone mutation affects the function of SETD2 at the nucleosome level, we determined the cryo-EM structure of human SETD2 associated with an H3.3K36M nucleosome and cofactor S-adenosylmethionine (SAM), and revealed that SETD2 is attached to the N-terminal region of histone H3 and the nucleosome DNA at superhelix location 1, accompanied with the partial unwrapping of nucleosome DNA to expose the SETD2-binding site. These structural features were also observed in the previous cryo-EM structure of the fungal Set2-nucleosome complex. By contrast with the stable association of SETD2 with the H3.3K36M nucleosome, the EM densities of SETD2 could not be observed on the wild-type nucleosome surface, suggesting that the association of SETD2 with wild-type nucleosome might be transient. The linker histone H1, which stabilizes the wrapping of nucleosome DNA at the entry/exit sites, exhibits an inhibitory effect on the activities of SETD2 and displays inversely correlated genome distributions with that of the H3K36me3 marks. Cryo-EM analysis of yeast H3K36 methyltransferase Set2 complexed with nucleosomes further revealed evolutionarily conserved structural features for nucleosome recognition in eukaryotes, and provides insights into the mechanism of activity regulation. These findings have advanced our understanding of the structural basis for the tumorigenesis mechanism of the H3.3K36M mutation and highlight the effect of nucleosome conformation on the regulation of histone modification. | ||||||||||||
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_31042.map.gz | 49.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-31042-v30.xml emd-31042.xml | 8.1 KB 8.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_31042.png | 43.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-31042 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31042 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_31042_validation.pdf.gz | 371.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_31042_full_validation.pdf.gz | 371.1 KB | 表示 | |
XML形式データ | emd_31042_validation.xml.gz | 5.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31042 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31042 | 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_31042.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: 1.09 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 : yeast Set2-NCP complex
全体 | 名称: yeast Set2-NCP complex |
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要素 |
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-超分子 #1: yeast Set2-NCP complex
超分子 | 名称: yeast Set2-NCP complex / タイプ: complex / ID: 1 / 親要素: 0 |
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由来(天然) | 生物種: Xenopus laevis (アフリカツメガエル) |
組換発現 | 生物種: Escherichia coli (大腸菌) |
分子量 | 実験値: 200 KDa |
-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 | 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: 1.5625 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: FLOOD BEAM / 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
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 177138 |
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初期 角度割当 | タイプ: ANGULAR RECONSTITUTION |
最終 角度割当 | タイプ: ANGULAR RECONSTITUTION |