+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-13009 | |||||||||
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タイトル | Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2) | |||||||||
マップデータ | The main map. | |||||||||
試料 |
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キーワード | transcription / DNA repair | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / : / B-WICH complex / single strand break repair / regulation of transcription elongation by RNA polymerase II / DNA protection / positive regulation by virus of viral protein levels in host cell / B-WICH complex positively regulates rRNA expression ...negative regulation of double-strand break repair via nonhomologous end joining / regulation of transcription-coupled nucleotide-excision repair / nucleotide-excision repair complex / : / B-WICH complex / single strand break repair / regulation of transcription elongation by RNA polymerase II / DNA protection / positive regulation by virus of viral protein levels in host cell / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / epigenetic programming in the zygotic pronuclei / spindle assembly involved in female meiosis / double-strand break repair via classical nonhomologous end joining / photoreceptor cell maintenance / response to superoxide / Cul4-RING E3 ubiquitin ligase complex / UV-damage excision repair / positive regulation of DNA-templated transcription, elongation / response to UV-B / RNA polymerase binding / biological process involved in interaction with symbiont / ATP-dependent chromatin remodeler activity / positive regulation of transcription by RNA polymerase III / 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 / organelle membrane / positive regulation of transcription by RNA polymerase I / protein tyrosine kinase activator activity / RNA polymerase III activity / negative regulation of reproductive process / negative regulation of developmental process / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / site of DNA damage / RNA Polymerase I Transcription Initiation / cullin family protein binding / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / RNA polymerase II activity / viral release from host cell / response to X-ray / positive regulation of double-strand break repair via homologous recombination / pyrimidine dimer repair / transcription elongation by RNA polymerase I / positive regulation of transcription initiation by RNA polymerase II / ectopic germ cell programmed cell death / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / proteasomal protein catabolic process / positive regulation of translational initiation / ATP-dependent activity, acting on DNA / protein autoubiquitination / transcription-coupled nucleotide-excision repair / positive regulation of viral genome replication / RNA polymerase II, core complex / response to UV / JNK cascade / positive regulation of gluconeogenesis / translation initiation factor binding / positive regulation of DNA repair / neurogenesis / positive regulation of RNA splicing / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / transcription elongation factor complex / regulation of DNA-templated transcription elongation / DNA damage checkpoint signaling / helicase activity / promoter-specific chromatin binding / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter 類似検索 - 分子機能 | |||||||||
生物種 | Sus scrofa (ブタ) / 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: 2.7 Å | |||||||||
データ登録者 | Kokic G / Cramer P | |||||||||
資金援助 | ドイツ, 2件
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引用 | ジャーナル: Nature / 年: 2021 タイトル: Structural basis of human transcription-DNA repair coupling. 著者: Goran Kokic / Felix R Wagner / Aleksandar Chernev / Henning Urlaub / Patrick Cramer / 要旨: Transcription-coupled DNA repair removes bulky DNA lesions from the genome and protects cells against ultraviolet (UV) irradiation. Transcription-coupled DNA repair begins when RNA polymerase II ...Transcription-coupled DNA repair removes bulky DNA lesions from the genome and protects cells against ultraviolet (UV) irradiation. Transcription-coupled DNA repair begins when RNA polymerase II (Pol II) stalls at a DNA lesion and recruits the Cockayne syndrome protein CSB, the E3 ubiquitin ligase, CRL4 and UV-stimulated scaffold protein A (UVSSA). Here we provide five high-resolution structures of Pol II transcription complexes containing human transcription-coupled DNA repair factors and the elongation factors PAF1 complex (PAF) and SPT6. Together with biochemical and published data, the structures provide a model for transcription-repair coupling. Stalling of Pol II at a DNA lesion triggers replacement of the elongation factor DSIF by CSB, which binds to PAF and moves upstream DNA to SPT6. The resulting elongation complex, EC, uses the CSA-stimulated translocase activity of CSB to pull on upstream DNA and push Pol II forward. If the lesion cannot be bypassed, CRL4 spans over the Pol II clamp and ubiquitylates the RPB1 residue K1268, enabling recruitment of TFIIH to UVSSA and DNA repair. Conformational changes in CRL4 lead to ubiquitylation of CSB and to release of transcription-coupled DNA repair factors before transcription may continue over repaired 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_13009.map.gz | 95.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-13009-v30.xml emd-13009.xml | 55 KB 55 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_13009_fsc.xml | 14.1 KB | 表示 | FSCデータファイル |
画像 | emd_13009.png | 150.5 KB | ||
マスクデータ | emd_13009_msk_1.map emd_13009_msk_2.map emd_13009_msk_3.map emd_13009_msk_4.map | 244.1 MB 244.1 MB 244.1 MB 244.1 MB | マスクマップ | |
Filedesc metadata | emd-13009.cif.gz | 12.4 KB | ||
その他 | emd_13009_additional_1.map.gz emd_13009_additional_2.map.gz emd_13009_additional_3.map.gz emd_13009_additional_4.map.gz emd_13009_additional_5.map.gz emd_13009_additional_6.map.gz emd_13009_half_map_1.map.gz emd_13009_half_map_2.map.gz | 195.8 MB 195.8 MB 194 MB 193.8 MB 194.6 MB 193.8 MB 221 MB 220.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-13009 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13009 | 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_13009.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | The main map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.05 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
+マスク #1
+マスク #2
+マスク #3
+マスク #4
+追加マップ: Half map corresponding to the map focused refined on Pol II.
+追加マップ: Half map corresponding to the map focused refined on Pol II.
+追加マップ: Half map corresponding to the map focused refined on CSA-DDB1.
+追加マップ: Half map corresponding to the map focused refined on CSA-DDB1.
+追加マップ: Half map corresponding to the map focused refined on CSB.
+追加マップ: Half map corresponding to the map focused refined on CSB.
+ハーフマップ: Half map corresponding to the main map.
+ハーフマップ: Half map corresponding to the main map.
-試料の構成要素
+全体 : Complex between the transcribing RNA polymerase II and TCR factor...
+超分子 #1: Complex between the transcribing RNA polymerase II and TCR factor...
+超分子 #2: DNA-directed RNA polymerase with RNA_pol_L_2 and RNA polymerase
+超分子 #3: DNA excision repair protein ERCC-6 and ERCC-8, DNA damage-binding...
+超分子 #4: NTS, RNA, TS
+分子 #1: DNA-directed RNA polymerase II subunit RPB1
+分子 #2: DNA-directed RNA polymerase subunit beta
+分子 #3: DNA-directed RNA polymerase II subunit RPB3
+分子 #4: RPOL4c domain-containing protein
+分子 #5: DNA-directed RNA polymerase II subunit E
+分子 #6: DNA-directed RNA polymerase II subunit F
+分子 #7: DNA-directed RNA polymerase II subunit RPB7
+分子 #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #9: DNA-directed RNA polymerase II subunit RPB9
+分子 #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #11: RNA_pol_L_2 domain-containing protein
+分子 #12: RNA polymerase II subunit K
+分子 #13: DNA excision repair protein ERCC-6
+分子 #14: DNA damage-binding protein 1
+分子 #18: DNA excision repair protein ERCC-8
+分子 #15: NTS
+分子 #16: TS
+分子 #17: RNA
+分子 #19: ZINC ION
+分子 #20: MAGNESIUM ION
+分子 #21: ADENOSINE-5'-DIPHOSPHATE
+分子 #22: BERYLLIUM TRIFLUORIDE 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
濃度 | 0.3 mg/mL |
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緩衝液 | pH: 7.5 |
グリッド | モデル: Quantifoil R2/1 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 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 K3 (6k x 4k) / 撮影したグリッド数: 1 / 実像数: 10940 / 平均電子線量: 41.2 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 |