+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-16838 | ||||||||||||
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タイトル | Structure of the mammalian Pol II-Elongin complex, lacking the ELOA latch (composite map 1 for structure 2) | ||||||||||||
マップデータ | Composite map 2 for the Pol II-Elongin high resolution model | ||||||||||||
試料 |
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キーワード | Transcription elongation / Elongin / RNA polymerase II (RNAポリメラーゼII) / TRANSCRIPTION (転写 (生物学)) | ||||||||||||
機能・相同性 | 機能・相同性情報 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 ...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 / target-directed miRNA degradation / elongin complex / VCB complex / Cul5-RING ubiquitin ligase complex / : / Cul2-RING ubiquitin ligase complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / site of DNA damage / organelle membrane / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / transcription by RNA polymerase I / transcription by RNA polymerase III / Tat-mediated elongation of the HIV-1 transcript / RNA polymerase II activity / transcription-coupled nucleotide-excision repair / Formation of HIV-1 elongation complex containing HIV-1 Tat / RNA polymerase I complex / RNA polymerase III complex / Formation of HIV elongation complex in the absence of HIV Tat / RNA polymerase II, core complex / translation initiation factor binding / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / Evasion by RSV of host interferon responses / RNA Polymerase II Pre-transcription Events / DNA-directed RNA polymerase complex / positive regulation of RNA splicing / transcription corepressor binding / transcription elongation by RNA polymerase II / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / TP53 Regulates Transcription of DNA Repair Genes / Vif-mediated degradation of APOBEC3G / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Inactivation of CSF3 (G-CSF) signaling / ribonucleoside binding / 核小体 / Regulation of expression of SLITs and ROBOs / DNA-directed 5'-3' RNA polymerase activity / ポリメラーゼ / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / protein-macromolecule adaptor activity / 染色体 / Neddylation / 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 / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / transcription by RNA polymerase II / nucleic acid binding / chromosome, telomeric region / protein dimerization activity / protein ubiquitination / nuclear speck / RNA依存性RNAポリメラーゼ / nucleotide binding / DNA-templated transcription / ubiquitin protein ligase binding / chromatin binding / regulation of transcription by RNA polymerase II / 核小体 / DNA binding / extracellular space / zinc ion binding / 核質 / metal ion binding / 細胞核 / 細胞質基質 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) / Sus scrofa (ブタ) / 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: 2.8 Å | ||||||||||||
データ登録者 | Chen Y / Kokic G / Dienemann C / Dybkov O / Urlaub H / Cramer P | ||||||||||||
資金援助 | European Union, ドイツ, 3件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2023 タイトル: Structure of the transcribing RNA polymerase II-Elongin complex. 著者: Ying Chen / Goran Kokic / Christian Dienemann / Olexandr Dybkov / Henning Urlaub / Patrick Cramer / 要旨: Elongin is a heterotrimeric elongation factor for RNA polymerase (Pol) II transcription that is conserved among metazoa. Here, we report three cryo-EM structures of human Elongin bound to ...Elongin is a heterotrimeric elongation factor for RNA polymerase (Pol) II transcription that is conserved among metazoa. Here, we report three cryo-EM structures of human Elongin bound to transcribing Pol II. The structures show that Elongin subunit ELOA binds the RPB2 side of Pol II and anchors the ELOB-ELOC subunit heterodimer. ELOA contains a 'latch' that binds between the end of the Pol II bridge helix and funnel helices, thereby inducing a conformational change near the polymerase active center. The latch is required for the elongation-stimulatory activity of Elongin, but not for Pol II binding, indicating that Elongin functions by allosterically regulating the conformational mobility of the polymerase active center. Elongin binding to Pol II is incompatible with association of the super elongation complex, PAF1 complex and RTF1, which also contain an elongation-stimulatory latch element. | ||||||||||||
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_16838.map.gz | 304 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-16838-v30.xml emd-16838.xml | 32.8 KB 32.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_16838.png | 111.2 KB | ||
Filedesc metadata | emd-16838.cif.gz | 10.5 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-16838 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16838 | 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_16838.map.gz / 形式: CCP4 / 大きさ: 325 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Composite map 2 for the Pol II-Elongin high resolution 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:
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-添付データ
-試料の構成要素
+全体 : The Pol II-Elongin transcription elongation complex
+超分子 #1: The Pol II-Elongin transcription elongation complex
+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: 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: 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: DNA-directed RNA polymerase II subunit RPB11-a
+分子 #12: RNA polymerase II subunit K
+分子 #16: Elongin-A
+分子 #17: Elongin-C
+分子 #18: Elongin-B
+分子 #13: Non-template DNA
+分子 #15: Template DNA
+分子 #14: RNA
+分子 #19: MAGNESIUM ION
+分子 #20: 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: 7.5 |
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グリッド | モデル: Quantifoil R3.5/1 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 2.1 |
凍結 | 凍結剤: ETHANE / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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 FIELDBright-field microscopy / 最大 デフォーカス(公称値): 7.5 µm 最小 デフォーカス(公称値): 0.35000000000000003 µm |
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: 40.09 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: NONE |
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初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.8 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION / 使用した粒子像数: 136189 |
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: OTHER |
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得られたモデル | PDB-8oew: |