+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-22588 | |||||||||
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タイトル | Structure of TFIIH/Rad4-Rad23-Rad33/DNA in DNA opening | |||||||||
マップデータ | Composite map after multibody refinement of TFIIH/Rad4-Rad23-Rad33/DNA with separate refinement of TFIIH and Rad4-23-33/DNA bodies | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / DNA translocase activity ...nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / DNA translocase activity / nucleotide-excision repair, preincision complex assembly / transcription open complex formation at RNA polymerase II promoter / DNA 5'-3' helicase / transcriptional start site selection at RNA polymerase II promoter / phosphatidylinositol-3-phosphate binding / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / DNA 3'-5' helicase / transcription preinitiation complex / DNA duplex unwinding / poly(A)+ mRNA export from nucleus / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / 3'-5' DNA helicase activity / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription by RNA polymerase I / DNA topological change / ATPase activator activity / Dual incision in TC-NER / ATP-dependent activity, acting on DNA / mismatch repair / DNA helicase activity / isomerase activity / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / ubiquitin protein ligase activity / double-stranded DNA binding / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / damaged DNA binding / DNA repair / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) / Baker's yeast (パン酵母) / 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: 9.25 Å | |||||||||
データ登録者 | van Eeuwen T / Min JH / Murakami K | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nat Commun / 年: 2021 タイトル: Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair. 著者: Trevor van Eeuwen / Yoonjung Shim / Hee Jong Kim / Tingting Zhao / Shrabani Basu / Benjamin A Garcia / Craig D Kaplan / Jung-Hyun Min / Kenji Murakami / 要旨: The versatile nucleotide excision repair (NER) pathway initiates as the XPC-RAD23B-CETN2 complex first recognizes DNA lesions from the genomic DNA and recruits the general transcription factor ...The versatile nucleotide excision repair (NER) pathway initiates as the XPC-RAD23B-CETN2 complex first recognizes DNA lesions from the genomic DNA and recruits the general transcription factor complex, TFIIH, for subsequent lesion verification. Here, we present a cryo-EM structure of an NER initiation complex containing Rad4-Rad23-Rad33 (yeast homologue of XPC-RAD23B-CETN2) and 7-subunit coreTFIIH assembled on a carcinogen-DNA adduct lesion at 3.9-9.2 Å resolution. A ~30-bp DNA duplex could be mapped as it straddles between Rad4 and the Ssl2 (XPB) subunit of TFIIH on the 3' and 5' side of the lesion, respectively. The simultaneous binding with Rad4 and TFIIH was permitted by an unwinding of DNA at the lesion. Translocation coupled with torque generation by Ssl2 and Rad4 would extend the DNA unwinding at the lesion and deliver the damaged strand to Rad3 (XPD) in an open form suitable for subsequent lesion scanning and verification. | |||||||||
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_22588.map.gz | 10.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-22588-v30.xml emd-22588.xml | 34.2 KB 34.2 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_22588_fsc.xml | 10.8 KB | 表示 | FSCデータファイル |
画像 | emd_22588.png | 44.9 KB | ||
その他 | emd_22588_additional_1.map.gz emd_22588_additional_2.map.gz emd_22588_half_map_1.map.gz emd_22588_half_map_2.map.gz | 59.7 MB 75.8 MB 77.6 MB 77.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-22588 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22588 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_22588_validation.pdf.gz | 727.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_22588_full_validation.pdf.gz | 727.2 KB | 表示 | |
XML形式データ | emd_22588_validation.xml.gz | 17.6 KB | 表示 | |
CIF形式データ | emd_22588_validation.cif.gz | 23.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22588 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22588 | 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_22588.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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注釈 | Composite map after multibody refinement of TFIIH/Rad4-Rad23-Rad33/DNA with separate refinement of TFIIH and Rad4-23-33/DNA bodies | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.08 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
-追加マップ: Map of Rad4-23-33/DNA body from multibody refinement of...
ファイル | emd_22588_additional_1.map | ||||||||||||
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注釈 | Map of Rad4-23-33/DNA body from multibody refinement of TFIIH/Rad4-Rad23-Rad33/DNA complex | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Map of TFIIH body from multibody refinement of...
ファイル | emd_22588_additional_2.map | ||||||||||||
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注釈 | Map of TFIIH body from multibody refinement of TFIIH/Rad4-Rad23-Rad33/DNA complex | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Unfiltered half map of TFIIH body from multibody...
ファイル | emd_22588_half_map_1.map | ||||||||||||
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注釈 | Unfiltered half map of TFIIH body from multibody refinement of TFIIH/Rad4-Rad23-Rad33/DNA complex. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Unfiltered half map of TFIIH body from multibody...
ファイル | emd_22588_half_map_2.map | ||||||||||||
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注釈 | Unfiltered half map of TFIIH body from multibody refinement of TFIIH/Rad4-Rad23-Rad33/DNA complex. | ||||||||||||
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 : 10 component complex of Rad4-23, Rad33 and TFIIH on damaged DNA
+超分子 #1: 10 component complex of Rad4-23, Rad33 and TFIIH on damaged DNA
+分子 #1: DNA repair protein RAD33
+分子 #2: General transcription and DNA repair factor IIH subunit TFB2
+分子 #3: DNA repair helicase RAD3
+分子 #4: General transcription and DNA repair factor IIH subunit TFB1
+分子 #5: General transcription and DNA repair factor IIH subunit TFB4
+分子 #6: General transcription and DNA repair factor IIH subunit SSL1
+分子 #9: DNA repair protein RAD4
+分子 #10: DNA repair helicase RAD25
+分子 #11: RNA polymerase II transcription factor B subunit 5
+分子 #7: Damaged DNA strand
+分子 #8: Undamaged DNA strand
+分子 #12: CALCIUM ION
+分子 #13: IRON/SULFUR CLUSTER
+分子 #14: 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: 7.6 |
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER |
凍結 | 凍結剤: ETHANE / 装置: LEICA EM CPC / 詳細: Manually blotted by Leica EM CPC. |
-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: 50.0 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: SPOT SCAN / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |