+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-26551 | |||||||||
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タイトル | Mediator-PIC Early (Composite Model) | |||||||||
マップデータ | composite map of Med-PICearly | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 regulation of transcription from RNA polymerase II promoter by galactose / TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / meiotic gene conversion / positive regulation of invasive growth in response to glucose limitation / RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / TFIIH-class transcription factor complex binding / core mediator complex / galactose metabolic process ...regulation of transcription from RNA polymerase II promoter by galactose / TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / meiotic gene conversion / positive regulation of invasive growth in response to glucose limitation / RNA polymerase II complex recruiting activity / regulation of mRNA 3'-end processing / TFIIH-class transcription factor complex binding / core mediator complex / galactose metabolic process / 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 / transcriptional start site selection at RNA polymerase II promoter / mediator complex / RPB4-RPB7 complex / positive regulation of transcription regulatory region DNA binding / transcription factor TFIIF complex / : / positive regulation of transcription from RNA polymerase II promoter by galactose / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / 転写開始前複合体 / RNA Polymerase I Transcription Initiation / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / 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 / Formation of TC-NER Pre-Incision Complex / termination of RNA polymerase II transcription / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / RNA polymerase II general transcription initiation factor activity / 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 / termination of RNA polymerase III transcription / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / RNA polymerase II complex binding / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / protein phosphatase activator activity / tRNA transcription by RNA polymerase III / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / positive regulation of translational initiation / TFIID-class transcription factor complex binding / RNA polymerase II activity / TFIIB-class transcription factor binding / transcription-coupled nucleotide-excision repair / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / DNA修復 / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / translation initiation factor binding / RNA polymerase II preinitiation complex assembly / transcription repressor complex / TBP-class protein binding / transcription antitermination / P-body / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / DNA-templated transcription initiation / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / ポリメラーゼ / cytoplasmic stress granule / ペルオキシソーム / transcription corepressor activity / protein-macromolecule adaptor activity / single-stranded DNA binding / リボソーム生合成 / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / DNA recombination / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / nucleic acid binding / single-stranded RNA binding / transcription coactivator activity 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_26551.map.gz | 36.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-26551-v30.xml emd-26551.xml | 59.6 KB 59.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_26551.png | 96.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-26551 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26551 | HTTPS FTP |
-関連構造データ
関連構造データ | 7uioMC 7ui9C 7uicC 7uifC 7uigC 7uikC 7uilC 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_26551.map.gz / 形式: CCP4 / 大きさ: 918.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | composite map of Med-PICearly | ||||||||||||||||||||
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
-試料の構成要素
+全体 : Med-PICearly
+超分子 #1: Med-PICearly
+分子 #1: DNA (38-MER)
+分子 #2: DNA (37-MER)
+分子 #3: Mediator of RNA polymerase II transcription subunit 15
+分子 #4: Mediator of RNA polymerase II transcription subunit 2
+分子 #5: Mediator of RNA polymerase II transcription subunit 3
+分子 #6: Mediator of RNA polymerase II transcription subunit 14
+分子 #7: Mediator of RNA polymerase II transcription subunit 5
+分子 #8: Mediator of RNA polymerase II transcription subunit 16
+分子 #9: Regulatory protein GAL4
+分子 #10: Mediator of RNA polymerase II transcription subunit 20
+分子 #11: Mediator of RNA polymerase II transcription subunit 7
+分子 #12: Mediator of RNA polymerase II transcription subunit 8
+分子 #13: Mediator of RNA polymerase II transcription subunit 9
+分子 #14: Mediator of RNA polymerase II transcription subunit 10
+分子 #15: Mediator of RNA polymerase II transcription subunit 11
+分子 #16: Mediator of RNA polymerase II transcription subunit 17
+分子 #17: Mediator of RNA polymerase II transcription subunit 18
+分子 #18: Mediator of RNA polymerase II transcription subunit 19
+分子 #19: Mediator of RNA polymerase II transcription subunit 21
+分子 #20: Mediator of RNA polymerase II transcription subunit 22
+分子 #21: Mediator of RNA polymerase II transcription subunit 31
+分子 #22: DNA-directed RNA polymerase II subunit RPB1
+分子 #23: DNA-directed RNA polymerase II subunit RPB1
+分子 #24: DNA-directed RNA polymerase II subunit RPB2
+分子 #25: DNA-directed RNA polymerase II subunit RPB3
+分子 #26: DNA-directed RNA polymerase II subunit RPB4
+分子 #27: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+分子 #28: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+分子 #29: DNA-directed RNA polymerase II subunit RPB7
+分子 #30: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #31: DNA-directed RNA polymerase II subunit RPB9
+分子 #32: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #33: DNA-directed RNA polymerase II subunit RPB11
+分子 #34: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+分子 #35: Transcription initiation factor IIB
+分子 #36: Transcription initiation factor IIF subunit alpha
+分子 #37: Transcription initiation factor IIF subunit beta
+分子 #38: Transcription elongation factor S-II
+分子 #39: Mediator of RNA polymerase II transcription subunit 1
+分子 #40: Mediator of RNA polymerase II transcription subunit 4
+分子 #41: Mediator of RNA polymerase II transcription subunit 6
+分子 #42: ZINC ION
+分子 #43: THREONINE
+分子 #44: ALANINE
+分子 #45: ASPARTIC ACID
-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 | 0.1 mg/mL |
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緩衝液 | pH: 7.6 |
グリッド | モデル: Quantifoil / 前処理 - タイプ: PLASMA CLEANING / 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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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 FIELDBright-field microscopy / 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 |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均露光時間: 3.4 sec. / 平均電子線量: 42.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
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最終 角度割当 | タイプ: PROJECTION MATCHING |
最終 再構成 | 使用したクラス数: 1 / アルゴリズム: FOURIER SPACE / 解像度のタイプ: BY AUTHOR / 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 1102984 |