+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4764 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A | ||||||||||||||||||||||||
マップデータ | |||||||||||||||||||||||||
試料 |
| ||||||||||||||||||||||||
キーワード | DNA damage / Nucleosome / 6-4 photoproduct / DNA BINDING PROTEIN | ||||||||||||||||||||||||
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 / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding / ubiquitin ligase complex scaffold activity ...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 / Cul4A-RING E3 ubiquitin ligase complex / WD40-repeat domain binding / ubiquitin ligase complex scaffold activity / Cul4B-RING E3 ubiquitin ligase complex / negative regulation of reproductive process / negative regulation of developmental process / site of DNA damage / protein localization to CENP-A containing chromatin / cullin family protein binding / CENP-A containing nucleosome / viral release from host cell / negative regulation of tumor necrosis factor-mediated signaling pathway / pyrimidine dimer repair / Replacement of protamines by nucleosomes in the male pronucleus / arachidonate 15-lipoxygenase / arachidonate 15-lipoxygenase activity / ectopic germ cell programmed cell death / Packaging Of Telomere Ends / proteasomal protein catabolic process / protein autoubiquitination / lipoxygenase pathway / positive regulation of viral genome replication / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / telomere organization / arachidonate metabolic process / Chromatin modifying enzymes / lipid oxidation / Deposition of new CENPA-containing nucleosomes at the centromere / hepoxilin biosynthetic process / response to UV / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / linoleic acid metabolic process / Meiotic synapsis / Inhibition of DNA recombination at telomere / positive regulation of gluconeogenesis / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Interleukin-7 signaling / epigenetic regulation of gene expression / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / regulation of circadian rhythm / nucleotide-excision repair / Transcriptional regulation by small RNAs / TP53 Regulates Transcription of DNA Repair Genes / lipopolysaccharide binding / Transcriptional regulation of granulopoiesis / Recognition of DNA damage by PCNA-containing replication complex / HDMs demethylate histones / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage Recognition in GG-NER / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PKMTs methylate histone lysines / B-WICH complex positively regulates rRNA expression / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / heterochromatin formation / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / RMTs methylate histone arginines / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / Wnt signaling pathway / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / structural constituent of chromatin / protein polyubiquitination / positive regulation of protein catabolic process / rhythmic process / cell junction / UCH proteinases / cellular response to UV / nucleosome 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: 4.5 Å | ||||||||||||||||||||||||
データ登録者 | Matsumoto S / Cavadini S | ||||||||||||||||||||||||
資金援助 | スイス, 日本, 7件
| ||||||||||||||||||||||||
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 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_4764.map.gz | 95.4 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-4764-v30.xml emd-4764.xml | 29.7 KB 29.7 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_4764.png | 143.7 KB | ||
Filedesc metadata | emd-4764.cif.gz | 8.6 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4764 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4764 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_4764_validation.pdf.gz | 458.4 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_4764_full_validation.pdf.gz | 458 KB | 表示 | |
XML形式データ | emd_4764_validation.xml.gz | 6.6 KB | 表示 | |
CIF形式データ | emd_4764_validation.cif.gz | 7.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4764 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4764 | HTTPS FTP |
-関連構造データ
関連構造データ | 6r90MC 4762C 4763C 4765C 4766C 4767C 4768C 6r8yC 6r8zC 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) |
---|---|
類似構造データ |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_4764.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ボクセルのサイズ | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-試料の構成要素
+全体 : UV-DDB bound to a THF2 containing nucleosome class A
+超分子 #1: UV-DDB bound to a THF2 containing nucleosome class A
+超分子 #2: Histone H3.1, Histone H2A, Histone H2B
+超分子 #3: Histone H4
+超分子 #4: DNA
+超分子 #5: DNA damage-binding protein 1(2), DNA damage-binding protein 2
+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 #7: DNA damage-binding protein 1
+分子 #8: DNA damage-binding protein 2
+分子 #5: Human alpha-satellite DNA (145-MER)
+分子 #6: Human alpha-satellite DNA (145-MER) with abasic sites at position...
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
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 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
緩衝液 | pH: 7.4 構成要素:
| ||||||||||||
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 |
---|---|
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 |
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 |
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 FIELD / Cs: 0.0 mm / 倍率(公称値): 130000 |
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 |
-画像解析
初期モデル | モデルのタイプ: OTHER |
---|---|
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 4.5 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: 128763 |
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 |
-原子モデル構築 1
初期モデル |
| ||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT | ||||||||||||||||||||||||||
得られたモデル | PDB-6r90: |