+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-28915 | |||||||||
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タイトル | SIRT6 bound to an H3K9Ac nucleosome | |||||||||
マップデータ | map A | |||||||||
試料 |
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キーワード | nucleosome / SIRTUIN6 / histone deacylation / H3K9Ac / GENE REGULATION | |||||||||
機能・相同性 | 機能・相同性情報 NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / ketone biosynthetic process / regulation of lipid catabolic process / NAD+-protein-lysine ADP-ribosyltransferase activity / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity ...NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / ketone biosynthetic process / regulation of lipid catabolic process / NAD+-protein-lysine ADP-ribosyltransferase activity / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / positive regulation of protein localization to chromatin / chromosome, subtelomeric region / DNA damage sensor activity / positive regulation of stem cell differentiation / positive regulation of blood vessel branching / NAD-dependent protein lysine deacetylase activity / retrotransposon silencing / protein acetyllysine N-acetyltransferase / cardiac muscle cell differentiation / positive regulation of chondrocyte proliferation / pericentric heterochromatin formation / positive regulation of telomere maintenance / NAD-dependent histone deacetylase activity / protein deacetylation / negative regulation of glucose import / protein localization to site of double-strand break / TORC2 complex binding / negative regulation of glycolytic process / negative regulation of protein localization to chromatin / lncRNA binding / DNA repair-dependent chromatin remodeling / positive regulation of double-strand break repair / positive regulation of vascular endothelial cell proliferation / negative regulation of protein import into nucleus / regulation of double-strand break repair via homologous recombination / positive regulation of fat cell differentiation / negative regulation of gene expression, epigenetic / positive regulation of stem cell population maintenance / regulation of protein secretion / positive regulation of stem cell proliferation / negative regulation of transcription elongation by RNA polymerase II / NAD+-protein ADP-ribosyltransferase activity / negative regulation of cellular senescence / site of DNA damage / regulation of lipid metabolic process / NAD+-protein poly-ADP-ribosyltransferase activity / 転移酵素; グリコシル基を移すもの; 五炭糖残基を移すもの / NAD+ binding / subtelomeric heterochromatin formation / nucleosome binding / regulation of protein localization to plasma membrane / negative regulation of gluconeogenesis / pericentric heterochromatin / response to UV / 転移酵素; アシル基を移すもの; アミノアシル基以外のアシル基を移すもの / nucleotidyltransferase activity / positive regulation of protein export from nucleus / determination of adult lifespan / regulation of circadian rhythm / circadian regulation of gene expression / protein destabilization / base-excision repair / positive regulation of insulin secretion / chromatin DNA binding / Pre-NOTCH Transcription and Translation / positive regulation of fibroblast proliferation / structural constituent of chromatin / transcription corepressor activity / nucleosome / double-strand break repair / glucose homeostasis / Processing of DNA double-strand break ends / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nucleosome assembly / positive regulation of cold-induced thermogenesis / site of double-strand break / damaged DNA binding / chromatin remodeling / protein heterodimerization activity / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / DNA binding / zinc ion binding / nucleoplasm / nucleus 類似検索 - 分子機能 | |||||||||
生物種 | Xenopus laevis (アフリカツメガエル) / 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: 3.1 Å | |||||||||
データ登録者 | Markert J / Whedon S / Wang Z / Cole P / Farnung L | |||||||||
資金援助 | 1件
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引用 | ジャーナル: J Am Chem Soc / 年: 2023 タイトル: Structural Basis of Sirtuin 6-Catalyzed Nucleosome Deacetylation. 著者: Zhipeng A Wang / Jonathan W Markert / Samuel D Whedon / Maheeshi Yapa Abeywardana / Kwangwoon Lee / Hanjie Jiang / Carolay Suarez / Hening Lin / Lucas Farnung / Philip A Cole / 要旨: The reversible acetylation of histone lysine residues is controlled by the action of acetyltransferases and deacetylases (HDACs), which regulate chromatin structure and gene expression. The sirtuins ...The reversible acetylation of histone lysine residues is controlled by the action of acetyltransferases and deacetylases (HDACs), which regulate chromatin structure and gene expression. The sirtuins are a family of NAD-dependent HDAC enzymes, and one member, sirtuin 6 (Sirt6), influences DNA repair, transcription, and aging. Here, we demonstrate that Sirt6 is efficient at deacetylating several histone H3 acetylation sites, including its canonical site Lys9, in the context of nucleosomes but not free acetylated histone H3 protein substrates. By installing a chemical warhead at the Lys9 position of histone H3, we trap a catalytically poised Sirt6 in complex with a nucleosome and employ this in cryo-EM structural analysis. The structure of Sirt6 bound to a nucleosome reveals extensive interactions between distinct segments of Sirt6 and the H2A/H2B acidic patch and nucleosomal DNA, which accounts for the rapid deacetylation of nucleosomal H3 sites and the disfavoring of histone H2B acetylation sites. These findings provide a new framework for understanding how HDACs target and regulate chromatin. | |||||||||
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_28915.map.gz | 150.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-28915-v30.xml emd-28915.xml | 30.3 KB 30.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_28915_fsc.xml | 11.6 KB | 表示 | FSCデータファイル |
画像 | emd_28915.png | 58.7 KB | ||
マスクデータ | emd_28915_msk_1.map | 163.6 MB | マスクマップ | |
Filedesc metadata | emd-28915.cif.gz | 6.7 KB | ||
その他 | emd_28915_additional_1.map.gz emd_28915_additional_2.map.gz emd_28915_additional_3.map.gz emd_28915_additional_4.map.gz emd_28915_half_map_1.map.gz emd_28915_half_map_2.map.gz | 151.9 MB 154.4 MB 3.2 MB 151.8 MB 151.9 MB 151.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-28915 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28915 | HTTPS FTP |
-関連構造データ
関連構造データ | 8f86MC 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_28915.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 | map A | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.83 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
-マスク #1
ファイル | emd_28915_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: half map 2 for map B
ファイル | emd_28915_additional_1.map | ||||||||||||
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注釈 | half map 2 for map B | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: map B
ファイル | emd_28915_additional_2.map | ||||||||||||
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注釈 | map B | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: mask for map B
ファイル | emd_28915_additional_3.map | ||||||||||||
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注釈 | mask for map B | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: half map 1 for map B
ファイル | emd_28915_additional_4.map | ||||||||||||
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注釈 | half map 1 for map 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 map 2 for map A
ファイル | emd_28915_half_map_1.map | ||||||||||||
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注釈 | half map 2 for map A | ||||||||||||
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 map 1 for map A
ファイル | emd_28915_half_map_2.map | ||||||||||||
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注釈 | half map 1 for map 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 : SIRT6 bound to H3K9Ac
+超分子 #1: SIRT6 bound to H3K9Ac
+分子 #1: Histone H3.2
+分子 #2: Histone H4
+分子 #3: Histone H2A type 1
+分子 #4: Histone H2B
+分子 #7: NAD-dependent protein deacylase sirtuin-6
+分子 #5: DNA (148-MER)
+分子 #6: DNA (148-MER)
+分子 #8: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl...
+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 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 50.45 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 / 最大 デフォーカス(公称値): 1.7 µm 最小 デフォーカス(公称値): 0.7000000000000001 µm |
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 | 空間: REAL / プロトコル: RIGID BODY FIT |
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得られたモデル | PDB-8f86: |