+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-15825 | |||||||||
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タイトル | Structure of the Pol II-TCR-ELOF1 complex. | |||||||||
マップデータ | Main, composite map. The maps used to make the main map are deposited as additional EM maps. | |||||||||
試料 |
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キーワード | DNA repair / ubiquitin / transcription / cryo-EM | |||||||||
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 / protein tyrosine kinase activator activity / 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 / protein tyrosine kinase activator activity / 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 / positive regulation of transcription by RNA polymerase I / RNA polymerase III activity / negative regulation of reproductive process / negative regulation of developmental process / RNA polymerase II complex binding / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / site of DNA damage / RNA Polymerase I Transcription Initiation / cullin family protein binding / 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 / positive regulation of DNA repair / 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 / ATP-dependent activity, acting on DNA / protein autoubiquitination / neurogenesis / transcription-coupled nucleotide-excision repair / positive regulation of viral genome replication / translation elongation factor activity / RNA polymerase II, core complex / response to UV / JNK cascade / positive regulation of gluconeogenesis / translation initiation factor binding / 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 / regulation of circadian rhythm / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / response to gamma radiation / Recognition of DNA damage by PCNA-containing replication complex / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Sus scrofa domesticus (ブタ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.6 Å | |||||||||
データ登録者 | Kokic G / Cramer P | |||||||||
資金援助 | ドイツ, European Union, 2件
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引用 | ジャーナル: To Be Published タイトル: Structure of the Pol II-TCR-ELOF1 complex. 著者: Kokic G / Cramer P | |||||||||
履歴 |
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-構造の表示
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 | emd_15825.map.gz | 80.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-15825-v30.xml emd-15825.xml | 54.1 KB 54.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_15825_fsc.xml | 14.8 KB | 表示 | FSCデータファイル |
画像 | emd_15825.png | 73.7 KB | ||
その他 | emd_15825_additional_1.map.gz emd_15825_additional_2.map.gz emd_15825_additional_3.map.gz emd_15825_additional_4.map.gz emd_15825_additional_5.map.gz emd_15825_additional_6.map.gz emd_15825_additional_7.map.gz emd_15825_half_map_1.map.gz emd_15825_half_map_2.map.gz | 251.8 MB 227 MB 252 MB 1.7 MB 227 MB 255.1 MB 242.9 MB 258.4 MB 258.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-15825 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15825 | HTTPS FTP |
-関連構造データ
関連構造データ | 8b3dMC 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 | 類似検索 - 機能・相同性F&H 検索 |
-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_15825.map.gz / 形式: CCP4 / 大きさ: 282.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Main, composite map. The maps used to make the main map are deposited as additional EM maps. | ||||||||||||||||||||
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:
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-添付データ
-追加マップ: Half map corresponding to the map focused refined on TCR-ELOF1.
ファイル | emd_15825_additional_1.map | ||||||||||||
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注釈 | Half map corresponding to the map focused refined on TCR-ELOF1. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Half map corresponding to the map focused refined on Pol II.
ファイル | emd_15825_additional_2.map | ||||||||||||
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注釈 | Half map corresponding to the map focused refined on Pol II. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Half map corresponding to the map focused refined on TCR-ELOF1.
ファイル | emd_15825_additional_3.map | ||||||||||||
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注釈 | Half map corresponding to the map focused refined on TCR-ELOF1. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Map focused refined on the UVSSA Zn-finger.
ファイル | emd_15825_additional_4.map | ||||||||||||
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注釈 | Map focused refined on the UVSSA Zn-finger. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Half map corresponding to the map focused refined on Pol II.
ファイル | emd_15825_additional_5.map | ||||||||||||
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注釈 | Half map corresponding to the map focused refined on Pol II. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Map focused refined on the UVSSA C-terminus.
ファイル | emd_15825_additional_6.map | ||||||||||||
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注釈 | Map focused refined on the UVSSA C-terminus. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Map focused refined on DDB1-CUL4A-RBX1.
ファイル | emd_15825_additional_7.map | ||||||||||||
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注釈 | Map focused refined on DDB1-CUL4A-RBX1. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map corresponding to the main map.
ファイル | emd_15825_half_map_1.map | ||||||||||||
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注釈 | Half map corresponding to the main map. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map corresponding to the main map.
ファイル | emd_15825_half_map_2.map | ||||||||||||
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注釈 | Half map corresponding to the main map. | ||||||||||||
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 : Pol II-TCR-ELOF1 complex.
+超分子 #1: Pol II-TCR-ELOF1 complex.
+分子 #1: DNA-directed RNA polymerase subunit
+分子 #2: DNA-directed RNA polymerase subunit beta
+分子 #3: DNA-directed RNA polymerase II subunit RPB3
+分子 #4: RNA polymerase II subunit D
+分子 #5: DNA-directed RNA polymerase II subunit E
+分子 #6: DNA-directed RNA polymerase II subunit F
+分子 #7: 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 1 homolog
+分子 #17: DNA excision repair protein ERCC-8
+分子 #18: DNA excision repair protein ERCC-6
+分子 #19: UV-stimulated scaffold protein A
+分子 #20: DNA damage-binding protein 1
+分子 #14: NTS
+分子 #16: TS
+分子 #15: RNA
+分子 #21: ZINC ION
+分子 #22: MAGNESIUM ION
+分子 #23: ADENOSINE-5'-DIPHOSPHATE
+分子 #24: 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
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
-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 BIOQUANTUM (6k x 4k) 平均電子線量: 42.0 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3.0 µm 最小 デフォーカス(公称値): 0.14400000000000002 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |