+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-12968 | |||||||||||||||
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タイトル | Structure of active transcription elongation complex Pol II-DSIF-ELL2-EAF1, Map 7, Focused map for Pol II core | |||||||||||||||
マップデータ | Focused map for Pol II core region (map7), used for generating the composite map 1 (Pol II-DSIF(SPT5-KOW5)-ELL2-EAF1 model) | |||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 super elongation complex / negative regulation of DNA-templated transcription, elongation / DSIF complex / snRNA transcription by RNA polymerase II / regulation of transcription elongation by RNA polymerase II / transcription elongation factor activity / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination ...super elongation complex / negative regulation of DNA-templated transcription, elongation / DSIF complex / snRNA transcription by RNA polymerase II / regulation of transcription elongation by RNA polymerase II / transcription elongation factor activity / 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 / positive regulation of DNA-templated transcription, elongation / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription elongation-coupled chromatin remodeling / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / intercellular bridge / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / : / : / negative regulation of transcription elongation by RNA polymerase II / RNA polymerase II complex binding / organelle membrane / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / positive regulation of macroautophagy / transcription elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / positive regulation of translational initiation / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / cis-regulatory region sequence-specific DNA binding / Formation of HIV elongation complex in the absence of HIV Tat / transcription-coupled nucleotide-excision repair / RNA polymerase III activity / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA polymerase II activity / Cajal body / translation initiation factor binding / RNA Polymerase II Pre-transcription Events / positive regulation of RNA splicing / transcription elongation factor complex / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / positive regulation of transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / fibrillar center / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / chromosome / single-stranded DNA binding / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エキソリボヌクレアーゼ / transcription by RNA polymerase II / nucleic acid binding / chromosome, telomeric region / single-stranded RNA binding / nuclear body / protein dimerization activity / hydrolase activity / nuclear speck / protein heterodimerization activity / RNA-directed RNA polymerase 類似検索 - 分子機能 | |||||||||||||||
生物種 | Sus scrofa (ブタ) / Homo sapiens (ヒト) / HIV whole-genome vector AA1305#18 (その他) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.8 Å | |||||||||||||||
データ登録者 | Chen Y / Vos SM / Dienemann C / Ninov M / Urlaub H / Cramer P | |||||||||||||||
資金援助 | ドイツ, 4件
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引用 | ジャーナル: Mol Cell / 年: 2021 タイトル: Allosteric transcription stimulation by RNA polymerase II super elongation complex. 著者: Ying Chen / Seychelle M Vos / Christian Dienemann / Momchil Ninov / Henning Urlaub / Patrick Cramer / 要旨: The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we ...The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we report the cryoelectron microscopy (cryo-EM) structure of ELL2-EAF1 bound to a RNA Pol II elongation complex at 2.8 Å resolution. The ELL2-EAF1 dimerization module directly binds the RNA Pol II lobe domain, explaining how SEC delivers P-TEFb to RNA Pol II. The same site on the lobe also binds the initiation factor TFIIF, consistent with SEC binding only after the transition from transcription initiation to elongation. Structure-guided functional analysis shows that the stimulation of RNA elongation requires the dimerization module and the ELL2 linker that tethers the module to the RNA Pol II protrusion. Our results show that SEC stimulates elongation allosterically and indicate that this stimulation involves stabilization of a closed conformation of the RNA Pol II active center cleft. | |||||||||||||||
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_12968.map.gz | 95.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-12968-v30.xml emd-12968.xml | 38.3 KB 38.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_12968_fsc.xml | 10.6 KB | 表示 | FSCデータファイル |
画像 | emd_12968.png | 115.4 KB | ||
マスクデータ | emd_12968_msk_1.map | 103 MB | マスクマップ | |
その他 | emd_12968_half_map_1.map.gz emd_12968_half_map_2.map.gz | 80.6 MB 80.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-12968 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12968 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_12968_validation.pdf.gz | 470.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_12968_full_validation.pdf.gz | 469.3 KB | 表示 | |
XML形式データ | emd_12968_validation.xml.gz | 17.9 KB | 表示 | |
CIF形式データ | emd_12968_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-12968 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12968 | 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_12968.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 | Focused map for Pol II core region (map7), used for generating the composite map 1 (Pol II-DSIF(SPT5-KOW5)-ELL2-EAF1 model) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
ファイル | emd_12968_msk_1.map | ||||||||||||
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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 1 for the focused map of Pol II map7 (EC core)
ファイル | emd_12968_half_map_1.map | ||||||||||||
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注釈 | half map 1 for the focused map of Pol II map7 (EC core) | ||||||||||||
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 1 for the focused map of Pol II map 7(EC core)
ファイル | emd_12968_half_map_2.map | ||||||||||||
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注釈 | half map 1 for the focused map of Pol II map 7(EC core) | ||||||||||||
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 : Transcription elongation complex of RNA polymerase II with elonga...
+超分子 #1: Transcription elongation complex of RNA polymerase II with elonga...
+超分子 #2: DNA-directed RNA polymerase
+超分子 #3: Elongation factors
+超分子 #4: RNA
+超分子 #5: Elongation factors
+分子 #1: DNA-directed RNA polymerase II subunit RPB1
+分子 #2: DNA-directed RNA polymerase II subunit beta
+分子 #3: DNA-directed RNA polymerase II subunit RPB3
+分子 #4: RNA polymerase II subunit D
+分子 #5: RNA polymerase II subunit E
+分子 #6: RNA polymerase II subunit F
+分子 #7: RNA polymerase II subunit G
+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: DNA-directed RNA polymerase II subunit RPB11
+分子 #12: RNA polymerase II subunit K
+分子 #13: RNA polymerase II elongation factor ELL2
+分子 #14: ELL-associated factor 1
+分子 #15: Transcription elongation factor SPT5
+分子 #16: Transcription elongation factor SPT4
+分子 #17: Template DNA
+分子 #18: Non-template DNA
+分子 #19: RNA
-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: 7.4 |
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凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 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 BIOQUANTUM (6k x 4k) 検出モード: COUNTING / 平均電子線量: 43.21 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 |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL |
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