+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-16610 | |||||||||
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タイトル | Yeast RNA polymerase II transcription pre-initiation complex with core Mediator | |||||||||
マップデータ | local resolution filtered map of raw reconstruction | |||||||||
試料 |
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キーワード | PIC / Mediator / TF / TRANSCRIPTION | |||||||||
機能・相同性 | 機能・相同性情報 regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / DNA translocase activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex ...regulation of mitotic recombination / RNA polymerase II promoter clearance / RNA polymerase II complex recruiting activity / positive regulation of mitotic recombination / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / DNA translocase activity / transcription open complex formation at RNA polymerase II promoter / transcriptional start site selection at RNA polymerase II promoter / RPB4-RPB7 complex / transcription factor TFIIF complex / DNA 5'-3' helicase / transcription factor TFIIA complex / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / DNA 3'-5' helicase / transcription preinitiation complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / poly(A)+ mRNA export from nucleus / RNA Polymerase I Transcription Initiation / DNA duplex unwinding / 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 / 3'-5' DNA helicase activity / 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 polymerase II general transcription initiation factor activity / RNA-templated transcription / RNA Polymerase II Pre-transcription Events / termination of RNA polymerase III transcription / Formation of TC-NER Pre-Incision Complex / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / termination of RNA polymerase I transcription / RNA Polymerase I Promoter Escape / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / Estrogen-dependent gene expression / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / transcription by RNA polymerase III / nuclear-transcribed mRNA catabolic process / RNA polymerase II activity / Dual incision in TC-NER / transcription elongation by RNA polymerase I / transcription-coupled nucleotide-excision repair / tRNA transcription by RNA polymerase III / RNA polymerase I activity / RNA polymerase I complex / RNA polymerase III complex / positive regulation of translational initiation / ATP-dependent activity, acting on DNA / translesion synthesis / RNA polymerase II, core complex / RNA polymerase II preinitiation complex assembly / translation initiation factor binding / DNA helicase activity / TBP-class protein binding / isomerase activity / DNA-templated transcription initiation / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / 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 / peroxisome / ribosome biogenesis / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / transcription by RNA polymerase II / nucleic acid binding / damaged DNA binding / single-stranded RNA binding / protein dimerization activity / mRNA binding / nucleotide binding / regulation of DNA-templated transcription / nucleolus / ATP hydrolysis activity / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / ATP binding / nucleus 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) / Synthetic construct (人工物) / 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: 3.0 Å | |||||||||
データ登録者 | Wang H / Schilbach S / Cramer P | |||||||||
資金援助 | European Union, ドイツ, 2件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2023 タイトル: Yeast PIC-Mediator structure with RNA polymerase II C-terminal domain. 著者: Sandra Schilbach / Haibo Wang / Christian Dienemann / Patrick Cramer / 要旨: For transcription initiation, RNA polymerase II (Pol II) forms a preinitiation complex (PIC) that associates with the general coactivator Mediator. Whereas atomic models of the human PIC-Mediator ...For transcription initiation, RNA polymerase II (Pol II) forms a preinitiation complex (PIC) that associates with the general coactivator Mediator. Whereas atomic models of the human PIC-Mediator structure have been reported, structures for its yeast counterpart remain incomplete. Here, we present an atomic model for the yeast PIC with core Mediator, including the Mediator middle module that was previously poorly resolved and including subunit Med1 that was previously lacking. We observe three peptide regions containing eleven of the 26 heptapeptide repeats of the flexible C-terminal repeat domain (CTD) of Pol II. Two of these CTD regions bind between the Mediator head and middle modules and form defined CTD-Mediator interactions. CTD peptide 1 binds between the Med6 shoulder and Med31 knob domains, whereas CTD peptide 2 forms additional contacts with Med4. The third CTD region (peptide 3) binds in the Mediator cradle and associates with the Mediator hook. Comparisons with the human PIC-Mediator structure show that the central region in peptide 1 is similar and forms conserved contacts with Mediator, whereas peptides 2 and 3 exhibit distinct structures and Mediator interactions. | |||||||||
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_16610.map.gz | 143.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-16610-v30.xml emd-16610.xml | 93.3 KB 93.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_16610_fsc.xml | 14.1 KB | 表示 | FSCデータファイル |
画像 | emd_16610.png | 195.4 KB | ||
Filedesc metadata | emd-16610.cif.gz | 19 KB | ||
その他 | emd_16610_additional_1.map.gz emd_16610_additional_2.map.gz emd_16610_additional_3.map.gz emd_16610_additional_4.map.gz emd_16610_additional_5.map.gz emd_16610_half_map_1.map.gz emd_16610_half_map_2.map.gz | 150.2 MB 219.8 MB 214.8 MB 215.1 MB 193.1 MB 193.9 MB 193.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-16610 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16610 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_16610_validation.pdf.gz | 837.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_16610_full_validation.pdf.gz | 836.6 KB | 表示 | |
XML形式データ | emd_16610_validation.xml.gz | 21.1 KB | 表示 | |
CIF形式データ | emd_16610_validation.cif.gz | 27.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16610 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16610 | HTTPS FTP |
-関連構造データ
関連構造データ | 8cenMC 8ceoC 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_16610.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | local resolution filtered map of raw reconstruction | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
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: composite map for model building
ファイル | emd_16610_additional_1.map | ||||||||||||
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注釈 | composite map for model building | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: focused refinement map of cPIC
ファイル | emd_16610_additional_2.map | ||||||||||||
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注釈 | focused refinement map of cPIC | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: focused refinement map of TFIIH
ファイル | emd_16610_additional_3.map | ||||||||||||
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注釈 | focused refinement map of TFIIH | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: focused refinement map of cMed
ファイル | emd_16610_additional_4.map | ||||||||||||
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注釈 | focused refinement map of cMed | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: focused refinement map of cMed-CTD
ファイル | emd_16610_additional_5.map | ||||||||||||
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注釈 | focused refinement map of cMed-CTD | ||||||||||||
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 2
ファイル | emd_16610_half_map_1.map | ||||||||||||
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注釈 | half map 2 | ||||||||||||
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
ファイル | emd_16610_half_map_2.map | ||||||||||||
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注釈 | half map 1 | ||||||||||||
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 : Yeast RNA polymerase II transcription pre-initiation complex with...
+超分子 #1: Yeast RNA polymerase II transcription pre-initiation complex with...
+超分子 #2: DNA-directed RNA polymerase subunits
+超分子 #3: General transcription and DNA repair factors, and RNA polymerase ...
+超分子 #4: DNA
+超分子 #5: Transcription initiation factors and Mediator of RNA polymerase I...
+分子 #1: General transcription and DNA repair factor IIH helicase subunit XPD
+分子 #2: General transcription and DNA repair factor IIH subunit TFB1
+分子 #3: General transcription and DNA repair factor IIH subunit TFB2
+分子 #4: RNA polymerase II transcription factor B subunit 3
+分子 #5: General transcription and DNA repair factor IIH subunit TFB4
+分子 #6: General transcription and DNA repair factor IIH subunit TFB5
+分子 #7: General transcription and DNA repair factor IIH subunit SSL1
+分子 #8: General transcription and DNA repair factor IIH helicase subunit XPB
+分子 #9: DNA-directed RNA polymerase II subunit RPB1
+分子 #10: DNA-directed RNA polymerase II subunit RPB2
+分子 #11: DNA-directed RNA polymerase II subunit RPB3
+分子 #12: DNA-directed RNA polymerase II subunit RPB4
+分子 #13: DNA-directed RNA polymerases I, II, and III subunit RPABC1
+分子 #14: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+分子 #15: DNA-directed RNA polymerase II subunit RPB7
+分子 #16: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+分子 #17: DNA-directed RNA polymerase II subunit RPB9
+分子 #18: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+分子 #19: DNA-directed RNA polymerase II subunit RPB11
+分子 #20: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+分子 #21: Transcription initiation factor IIB
+分子 #23: TATA-binding protein
+分子 #24: Transcription initiation factor IIF subunit alpha
+分子 #25: Transcription initiation factor IIF subunit beta
+分子 #27: Transcription initiation factor IIA large subunit
+分子 #28: Transcription initiation factor IIA subunit 2
+分子 #29: Transcription initiation factor IIE subunit alpha
+分子 #30: Transcription initiation factor IIE subunit beta
+分子 #31: Mediator of RNA polymerase II transcription subunit 6
+分子 #32: Mediator of RNA polymerase II transcription subunit 8
+分子 #33: Mediator of RNA polymerase II transcription subunit 11
+分子 #34: Mediator of RNA polymerase II transcription subunit 17
+分子 #35: Mediator of RNA polymerase II transcription subunit 18
+分子 #36: Mediator of RNA polymerase II transcription subunit 20
+分子 #37: Mediator of RNA polymerase II transcription subunit 22
+分子 #38: Mediator of RNA polymerase II transcription subunit 4
+分子 #39: Mediator of RNA polymerase II transcription subunit 7
+分子 #40: Mediator of RNA polymerase II transcription subunit 9
+分子 #41: Mediator of RNA polymerase II transcription subunit 10
+分子 #42: Mediator of RNA polymerase II transcription subunit 14
+分子 #43: Mediator of RNA polymerase II transcription subunit 19
+分子 #44: Mediator of RNA polymerase II transcription subunit 21
+分子 #45: Mediator of RNA polymerase II transcription subunit 31
+分子 #46: Mediator of RNA polymerase II transcription subunit 1
+分子 #22: NONTEMPLATE DNA (209-MER)
+分子 #26: TEMPLATE DNA (209-MER)
+分子 #47: IRON/SULFUR CLUSTER
+分子 #48: ZINC ION
+分子 #49: MAGNESIUM 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
濃度 | 0.2 mg/mL |
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緩衝液 | pH: 7.5 |
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): 2.0 µm / 最小 デフォーカス(公称値): 0.8 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |