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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-13016 | |||||||||
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タイトル | Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 5) | |||||||||
![]() | The main map. | |||||||||
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機能・相同性 | ![]() Prolactin receptor signaling / double-strand break repair via synthesis-dependent strand annealing / regulation of transcription-coupled nucleotide-excision repair / Regulation of BACH1 activity / negative regulation of double-strand break repair via nonhomologous end joining / Recognition of DNA damage by PCNA-containing replication complex / blastocyst growth / inner cell mass cell differentiation / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex ...Prolactin receptor signaling / double-strand break repair via synthesis-dependent strand annealing / regulation of transcription-coupled nucleotide-excision repair / Regulation of BACH1 activity / negative regulation of double-strand break repair via nonhomologous end joining / Recognition of DNA damage by PCNA-containing replication complex / blastocyst growth / inner cell mass cell differentiation / DNA Damage Recognition in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / Ski complex / Dual incision in TC-NER / positive regulation of mRNA 3'-end processing / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / nucleotide-excision repair complex / mRNA decay by 3' to 5' exoribonuclease / Regulation of RAS by GAPs / Regulation of RUNX2 expression and activity / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / RNA polymerase II C-terminal domain phosphoserine binding / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of DVL / Orc1 removal from chromatin / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Hedgehog 'on' state / negative regulation of granulocyte differentiation / regulation of isotype switching / Degradation of beta-catenin by the destruction complex / regulation of mRNA export from nucleus / regulation of muscle cell differentiation / Cdc73/Paf1 complex / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / eukaryotic initiation factor 4E binding / blastocyst hatching / Interleukin-1 signaling / positive regulation of cell cycle G1/S phase transition / KEAP1-NFE2L2 pathway / anaphase-promoting complex / GLI3 is processed to GLI3R by the proteasome / B-WICH complex / single strand break repair / trophectodermal cell differentiation / nucleosome organization / cullin-RING-type E3 NEDD8 transferase / regulation of mRNA processing / regulation of transcription elongation by RNA polymerase II / Neddylation / DNA translocase activity / Antigen processing: Ubiquitination & Proteasome degradation / cullin-RING ubiquitin ligase complex / DNA protection / positive regulation by virus of viral protein levels in host cell / regulation of DNA damage checkpoint / regulation of nucleotide-excision repair / 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 / mRNA 3'-end processing / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / 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 / double-strand break repair via classical nonhomologous end joining / spindle assembly involved in female meiosis / response to superoxide / photoreceptor cell maintenance / blastocyst formation / VCB complex / Cul4-RING E3 ubiquitin ligase complex / positive regulation of protein autoubiquitination / UV-damage excision repair 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.0 Å | |||||||||
![]() | Kokic G / Cramer P | |||||||||
資金援助 | ![]()
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![]() | ![]() 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 |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
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 | ![]() | 172 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 84.2 KB 84.2 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 14.9 KB | 表示 | ![]() |
画像 | ![]() | 130.8 KB | ||
マスクデータ | ![]() ![]() ![]() ![]() ![]() ![]() | 282.6 MB 282.6 MB 282.6 MB 282.6 MB 282.6 MB 282.6 MB | ![]() | |
その他 | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | 235.9 MB 224.8 MB 226.5 MB 227.1 MB 236 MB 226.9 MB 226.9 MB 225.1 MB 227.1 MB 240.1 MB 227.1 MB 240.1 MB 259.1 MB 257.8 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 562.7 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 562.2 KB | 表示 | |
XML形式データ | ![]() | 22.8 KB | 表示 | |
CIF形式データ | ![]() | 29.9 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
+マスク #5
+マスク #6
+追加マップ: Half map corresponding to the map focused refined...
+追加マップ: Half map corresponding to the map focused refined on PAF.
+追加マップ: Half map corresponding to the map focused refined on SPT6.
+追加マップ: Half map corresponding to the map focused refined on SPT6.
+追加マップ: Half map corresponding to the map focused refined...
+追加マップ: Half map corresponding to the map focused refined...
+追加マップ: Half map corresponding to the map focused refined...
+追加マップ: Half map corresponding to the map focused refined on PAF.
+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-CSB.
+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-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.
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試料の構成要素
+全体 : Transcribing Pol II bound to TRC factors, SPT6 and PAF.
+超分子 #1: Transcribing Pol II bound to TRC factors, SPT6 and PAF.
+超分子 #2: DNA-directed RNA polymerase with RNA_pol_L_2 and RNA polymerase
+超分子 #3: Supplementary proteins
+超分子 #4: NTS, RNA, TS
+超分子 #5: E3 ubiquitin-protein ligase RBX1
+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: Transcription elongation factor SPT6
+分子 #16: LEO1 helix
+分子 #17: RNA polymerase-associated protein CTR9 homolog
+分子 #19: RNA polymerase-associated protein LEO1
+分子 #20: RNA polymerase II-associated factor 1 homolog
+分子 #21: WD repeat-containing protein 61
+分子 #22: Parafibromin
+分子 #23: DNA excision repair protein ERCC-8
+分子 #24: DNA excision repair protein ERCC-6
+分子 #25: UV-stimulated scaffold protein A
+分子 #26: DNA damage-binding protein 1
+分子 #27: Cullin-4A
+分子 #28: E3 ubiquitin-protein ligase RBX1
+分子 #14: NTS
+分子 #18: TS
+分子 #15: RNA
+分子 #29: ZINC ION
+分子 #30: MAGNESIUM 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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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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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 |
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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: 40.4 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 倍率(公称値): 81000 |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |