+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4762 | ||||||||||||||||||||||||
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タイトル | Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB | ||||||||||||||||||||||||
マップデータ | |||||||||||||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex ...positive regulation by virus of viral protein levels in host cell / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / biological process involved in interaction with symbiont / regulation of mitotic cell cycle phase transition / WD40-repeat domain binding / Cul4A-RING E3 ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of reproductive process / negative regulation of developmental process / site of DNA damage / cullin family protein binding / viral release from host cell / pyrimidine dimer repair / negative regulation of tumor necrosis factor-mediated signaling pathway / ectopic germ cell programmed cell death / negative regulation of megakaryocyte differentiation / positive regulation of viral genome replication / protein autoubiquitination / protein localization to CENP-A containing chromatin / 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 / response to UV / 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 / positive regulation of gluconeogenesis / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNAメチル化 / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / proteasomal protein catabolic process / Recognition of DNA damage by PCNA-containing replication complex / nucleotide-excision repair / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / DNA Damage Recognition in GG-NER / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / Dual Incision in GG-NER / HDMs demethylate histones / regulation of circadian rhythm / DNA Damage/Telomere Stress Induced Senescence / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Metalloprotease DUBs / Formation of TC-NER Pre-Incision Complex / PKMTs methylate histone lysines / RMTs methylate histone arginines / Wntシグナル経路 / 遺伝的組換え / Pre-NOTCH Transcription and Translation / Formation of Incision Complex in GG-NER / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Dual incision in TC-NER / protein polyubiquitination / Gap-filling DNA repair synthesis and ligation in TC-NER / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / positive regulation of protein catabolic process / UCH proteinases / cellular response to UV / rhythmic process / ヌクレオソーム / antimicrobial humoral immune response mediated by antimicrobial peptide / protein-macromolecule adaptor activity / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / 細胞結合 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 遺伝子発現 類似検索 - 分子機能 | ||||||||||||||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.3 Å | ||||||||||||||||||||||||
データ登録者 | Matsumoto S / Cavadini S / Bunker RD / Thoma NH | ||||||||||||||||||||||||
資金援助 | スイス, 日本, 7件
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引用 | ジャーナル: Nature / 年: 2019 タイトル: DNA damage detection in nucleosomes involves DNA register shifting. 著者: Syota Matsumoto / Simone Cavadini / Richard D Bunker / Ralph S Grand / Alessandro Potenza / Julius Rabl / Junpei Yamamoto / Andreas D Schenk / Dirk Schübeler / Shigenori Iwai / Kaoru ...著者: Syota Matsumoto / Simone Cavadini / Richard D Bunker / Ralph S Grand / Alessandro Potenza / Julius Rabl / Junpei Yamamoto / Andreas D Schenk / Dirk Schübeler / Shigenori Iwai / Kaoru Sugasawa / Hitoshi Kurumizaka / Nicolas H Thomä / 要旨: Access to DNA packaged in nucleosomes is critical for gene regulation, DNA replication and DNA repair. In humans, the UV-damaged DNA-binding protein (UV-DDB) complex detects UV-light-induced ...Access to DNA packaged in nucleosomes is critical for gene regulation, DNA replication and DNA repair. In humans, the UV-damaged DNA-binding protein (UV-DDB) complex detects UV-light-induced pyrimidine dimers throughout the genome; however, it remains unknown how these lesions are recognized in chromatin, in which nucleosomes restrict access to DNA. Here we report cryo-electron microscopy structures of UV-DDB bound to nucleosomes bearing a 6-4 pyrimidine-pyrimidone dimer or a DNA-damage mimic in various positions. We find that UV-DDB binds UV-damaged nucleosomes at lesions located in the solvent-facing minor groove without affecting the overall nucleosome architecture. In the case of buried lesions that face the histone core, UV-DDB changes the predominant translational register of the nucleosome and selectively binds the lesion in an accessible, exposed position. Our findings explain how UV-DDB detects occluded lesions in strongly positioned nucleosomes, and identify slide-assisted site exposure as a mechanism by which high-affinity DNA-binding proteins can access otherwise occluded sites in nucleosomal DNA. | ||||||||||||||||||||||||
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_4762.map.gz | 91.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4762-v30.xml emd-4762.xml | 30 KB 30 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_4762.png | 70 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4762 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4762 | HTTPS FTP |
-関連構造データ
関連構造データ | 6r8yMC 4763C 4764C 4765C 4766C 4767C 4768C 6r8zC 6r90C 6r91C 6r92C 6r93C 6r94C 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 |
-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_4762.map.gz / 形式: CCP4 / 大きさ: 103 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: 0.86 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 : UV-DDB bound to a 6-4PP containing nucleosome
+超分子 #1: UV-DDB bound to a 6-4PP containing nucleosome
+超分子 #2: histones
+超分子 #3: DNA damage-binding proteins
+超分子 #4: DNA
+超分子 #5: histones
+分子 #1: Histone H3.1
+分子 #2: Histone H4
+分子 #3: Histone H2A type 1-B/E
+分子 #4: Histone H2B type 1-J
+分子 #5: Histone H4
+分子 #8: DNA damage-binding protein 1
+分子 #9: DNA damage-binding protein 2
+分子 #6: Human alpha-satellite DNA (145-MER)
+分子 #7: Human alpha-satellite DNA (145-MER) with a 6-4PP at positions 95-96
-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
濃度 | 2 mg/mL | ||||||||||||
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緩衝液 | pH: 7.4 構成要素:
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凍結 | 凍結剤: ETHANE / チャンバー内湿度: 85 % / チャンバー内温度: 277 K / 装置: LEICA EM GP |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 50.0 µm / 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 0.0 mm / 倍率(公称値): 130000 |
特殊光学系 | エネルギーフィルター - 名称: GIF Quantum LS / エネルギーフィルター - スリット幅: 20 eV |
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 |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 撮影したグリッド数: 1 / 平均露光時間: 6.0 sec. / 平均電子線量: 40.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
CTF補正 | ソフトウェア - 名称: Gctf |
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初期 角度割当 | タイプ: OTHER / ソフトウェア - 名称: RELION |
最終 角度割当 | タイプ: OTHER / ソフトウェア - 名称: RELION |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 4.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 2) / 使用した粒子像数: 84000 |
-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: FLEXIBLE FIT 当てはまり具合の基準: Cross-correlation coefficient | ||||||||||||||||||||||||||
得られたモデル | PDB-6r8y: |