+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-26542 | |||||||||
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タイトル | Core Mediator-PICearly (Copy A) | |||||||||
マップデータ | Core Mediator-PICearly (Copy A) - Unsharpened | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 meiotic gene conversion / RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / TFIIH-class transcription factor complex binding / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / RPB4-RPB7 complex / transcriptional start site selection at RNA polymerase II promoter ...meiotic gene conversion / RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / TFIIH-class transcription factor complex binding / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / RPB4-RPB7 complex / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / mediator complex / transcription preinitiation complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / TP53 Regulates Transcription of DNA Repair Genes / termination of RNA polymerase II transcription / 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-templated transcription / RNA Polymerase II Pre-transcription Events / RNA polymerase II general transcription initiation factor activity / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / RNA polymerase II complex binding / protein phosphatase activator activity / nucleolar large rRNA transcription by RNA polymerase I / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / TFIID-class transcription factor complex binding / nuclear-transcribed mRNA catabolic process / transcription by RNA polymerase III / TFIIB-class transcription factor binding / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / tRNA transcription by RNA polymerase III / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / cellular response to nutrient levels / positive regulation of translational initiation / transcription-coupled nucleotide-excision repair / RNA polymerase II, core complex / translesion synthesis / positive regulation of transcription elongation by RNA polymerase II / RNA polymerase II preinitiation complex assembly / transcription coregulator activity / translation initiation factor binding / TBP-class protein binding / transcription antitermination / DNA-templated transcription initiation / transcription initiation at RNA polymerase II promoter / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription elongation by RNA polymerase II / P-body / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / cytoplasmic stress granule / mRNA processing / transcription corepressor activity / ribosome biogenesis / peroxisome / protein-macromolecule adaptor activity / single-stranded DNA binding / cellular response to heat / DNA-binding transcription factor binding / DNA recombination / transcription coactivator activity / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / single-stranded RNA binding / protein dimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / DNA repair / DNA-templated transcription / mRNA binding / nucleotide binding / regulation of transcription by RNA polymerase II 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae S288C (パン酵母) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.3 Å | |||||||||
データ登録者 | Gorbea Colon JJ / Chen S-F / Tsai KL / Murakami K | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Mol Cell / 年: 2023 タイトル: Structural basis of a transcription pre-initiation complex on a divergent promoter. 著者: Jose J Gorbea Colón / Leon Palao / Shin-Fu Chen / Hee Jong Kim / Laura Snyder / Yi-Wei Chang / Kuang-Lei Tsai / Kenji Murakami / 要旨: Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single ...Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription. | |||||||||
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_26542.map.gz | 141 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-26542-v30.xml emd-26542.xml | 58.6 KB 58.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_26542_fsc.xml | 12.7 KB | 表示 | FSCデータファイル |
画像 | emd_26542.png | 41.7 KB | ||
マスクデータ | emd_26542_msk_1.map | 178 MB | マスクマップ | |
その他 | emd_26542_additional_1.map.gz emd_26542_additional_2.map.gz emd_26542_half_map_1.map.gz emd_26542_half_map_2.map.gz | 10.8 MB 165.1 MB 140.9 MB 140.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-26542 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26542 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_26542_validation.pdf.gz | 651.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_26542_full_validation.pdf.gz | 650.8 KB | 表示 | |
XML形式データ | emd_26542_validation.xml.gz | 19.7 KB | 表示 | |
CIF形式データ | emd_26542_validation.cif.gz | 25.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26542 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26542 | HTTPS FTP |
-関連構造データ
関連構造データ | 7ui9MC 7uicC 7uifC 7uigC 7uikC 7uilC 7uioC 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_26542.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Core Mediator-PICearly (Copy A) - Unsharpened | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.38 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
-マスク #1
ファイル | emd_26542_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 |
-追加マップ: Core Mediator-PICearly (Copy A) - Sharpened (DeepEMhancer)
ファイル | emd_26542_additional_1.map | ||||||||||||
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注釈 | Core Mediator-PICearly (Copy A) - Sharpened (DeepEMhancer) | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Core Mediator-PICearly (Copy A) - Sharpened (Relion)
ファイル | emd_26542_additional_2.map | ||||||||||||
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注釈 | Core Mediator-PICearly (Copy A) - Sharpened (Relion) | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Core Mediator-PICearly (Copy A) - Half Map 1
ファイル | emd_26542_half_map_1.map | ||||||||||||
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注釈 | Core Mediator-PICearly (Copy A) - Half Map 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Core Mediator-PICearly (Copy A) - Half Map 2
ファイル | emd_26542_half_map_2.map | ||||||||||||
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注釈 | Core Mediator-PICearly (Copy A) - Half Map 2 | ||||||||||||
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 : Core Mediator-PICearly (Copy A)
+超分子 #1: Core Mediator-PICearly (Copy A)
+分子 #1: Transcription initiation factor IIB
+分子 #2: Transcription initiation factor IIF subunit alpha
+分子 #3: Transcription initiation factor IIF subunit beta
+分子 #4: Transcription elongation factor S-II
+分子 #5: Mediator of RNA polymerase II transcription subunit 1
+分子 #6: Mediator of RNA polymerase II transcription subunit 4
+分子 #7: Mediator of RNA polymerase II transcription subunit 6
+分子 #8: Mediator of RNA polymerase II transcription subunit 7
+分子 #9: Mediator of RNA polymerase II transcription subunit 8
+分子 #10: Mediator of RNA polymerase II transcription subunit 9
+分子 #11: Mediator of RNA polymerase II transcription subunit 10
+分子 #12: Mediator of RNA polymerase II transcription subunit 11
+分子 #13: Mediator of RNA polymerase II transcription subunit 14
+分子 #14: Mediator of RNA polymerase II transcription subunit 17
+分子 #15: Mediator of RNA polymerase II transcription subunit 18
+分子 #16: Mediator of RNA polymerase II transcription subunit 19
+分子 #17: Mediator of RNA polymerase II transcription subunit 20
+分子 #18: Mediator of RNA polymerase II transcription subunit 21
+分子 #19: Mediator of RNA polymerase II transcription subunit 22
+分子 #20: Mediator of RNA polymerase II transcription subunit 31
+分子 #21: DNA-directed RNA polymerase II subunit RPB1
+分子 #22: DNA-directed RNA polymerase II subunit RPB1
+分子 #23: DNA-directed RNA polymerase II subunit RPB2
+分子 #24: DNA-directed RNA polymerase II subunit RPB3
+分子 #25: DNA-directed RNA polymerase II subunit RPB4
+分子 #26: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+分子 #27: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+分子 #28: DNA-directed RNA polymerase II subunit RPB7
+分子 #29: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #30: DNA-directed RNA polymerase II subunit RPB9
+分子 #31: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #32: DNA-directed RNA polymerase II subunit RPB11
+分子 #33: DNA-directed RNA polymerases I, II, and III subunit RPABC4
-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
濃度 | .1 mg/mL | |||||||||||||||
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緩衝液 | pH: 7.6 構成要素:
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グリッド | モデル: Quantifoil / 材質: COPPER / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 60 sec. | |||||||||||||||
凍結 | 凍結剤: ETHANE / 装置: 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) / 実像数: 40900 / 平均露光時間: 3.4 sec. / 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 | 最大 デフォーカス(補正後): 3.0 µm / 最小 デフォーカス(補正後): 0.5 µm / 倍率(補正後): 64000 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 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): 0.5 µm / 倍率(公称値): 64000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |