+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7nvr | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | Human Mediator with RNA Polymerase II Pre-initiation complex | ||||||||||||||||||
要素 |
| ||||||||||||||||||
キーワード | TRANSCRIPTION / Mediator complex / RNA polymerase II / TFIIH / Pre-initiation complex | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 negative regulation of smooth muscle cell differentiation / MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / : / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / positive regulation of core promoter binding / RNA polymerase II core complex assembly ...negative regulation of smooth muscle cell differentiation / MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / : / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / positive regulation of core promoter binding / RNA polymerase II core complex assembly / core mediator complex / meiotic sister chromatid cohesion / ventricular system development / hair follicle maturation / RNA polymerase transcription factor SL1 complex / hair cell differentiation / snRNA transcription by RNA polymerase II / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / UV protection / transcription factor TFIIK complex / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / 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 / RNA polymerase I core promoter sequence-specific DNA binding / transcriptional start site selection at RNA polymerase II promoter / 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 - 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 / mRNA Splicing - Major Pathway / transcription factor TFIIF complex / DNA 5'-3' helicase / mediator complex / RNA Polymerase III Abortive And Retractive Initiation / G protein-coupled receptor internalization / adult heart development / Generic Transcription Pathway / transcription factor TFIIA complex / female germ cell nucleus / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / male pronucleus / female pronucleus / cyclin-dependent protein serine/threonine kinase activator activity / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / germinal vesicle / nuclear vitamin D receptor binding / DNA 3'-5' helicase / [RNA-polymerase]-subunit kinase / limb development / transcription preinitiation complex / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / Signaling by FGFR2 IIIa TM / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of mitotic cell cycle phase transition / Viral Messenger RNA Synthesis / hematopoietic stem cell proliferation / 3'-5' DNA helicase activity / termination of RNA polymerase II transcription / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / cortical actin cytoskeleton / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIID complex / bone mineralization / RNA polymerase II general transcription initiation factor activity 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Homo sapiens (ヒト) Sus scrofa (ブタ) Trichoplusia ni (イラクサキンウワバ) Human mastadenovirus C (ウイルス) | ||||||||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.5 Å | ||||||||||||||||||
データ登録者 | Rengachari, S. / Schilbach, S. / Aibara, S. / Cramer, P. | ||||||||||||||||||
資金援助 | ドイツ, European Union, 5件
| ||||||||||||||||||
引用 | ジャーナル: Nature / 年: 2021 タイトル: Structures of mammalian RNA polymerase II pre-initiation complexes. 著者: Shintaro Aibara / Sandra Schilbach / Patrick Cramer / 要旨: The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) ...The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) assembles with general transcription factors into a pre-initiation complex (PIC) that opens promoter DNA. Previous work provided the molecular architecture of the yeast and human PIC and a topological model for DNA opening by the general transcription factor TFIIH. Here we report the high-resolution cryo-electron microscopy structure of PIC comprising human general factors and Sus scrofa domesticus Pol II, which is 99.9% identical to human Pol II. We determine the structures of PIC with closed and opened promoter DNA at 2.5-2.8 Å resolution, and resolve the structure of TFIIH at 2.9-4.0 Å resolution. We capture the TFIIH translocase XPB in the pre- and post-translocation states, and show that XPB induces and propagates a DNA twist to initiate the opening of DNA approximately 30 base pairs downstream of the TATA box. We also provide evidence that DNA opening occurs in two steps and leads to the detachment of TFIIH from the core PIC, which may stop DNA twisting and enable RNA chain initiation. | ||||||||||||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 7nvr.cif.gz | 2.2 MB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb7nvr.ent.gz | 1.7 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7nvr.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 7nvr_validation.pdf.gz | 1.6 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 7nvr_full_validation.pdf.gz | 1.6 MB | 表示 | |
XML形式データ | 7nvr_validation.xml.gz | 255.9 KB | 表示 | |
CIF形式データ | 7nvr_validation.cif.gz | 423.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/nv/7nvr ftp://data.pdbj.org/pub/pdb/validation_reports/nv/7nvr | HTTPS FTP |
-関連構造データ
関連構造データ | 12610MC 7nvsC 7nvtC 7nvuC 7nvvC 7nvwC 7nvxC 7nvyC 7nvzC 7nw0C M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
---|---|
類似構造データ |
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
+タンパク質 , 8種, 8分子 0389DKLO
+General transcription ... , 9種, 9分子 124567QRW
+DNA-directed RNA polymerase ... , 7種, 7分子 ABCEFGI
+DNA-directed RNA polymerases I, II, and III subunit ... , 2種, 2分子 HJ
+Transcription initiation factor ... , 4種, 4分子 MUVX
+DNA鎖 , 2種, 2分子 NT
+Unassigned peptide, likely ... , 2種, 2分子 YZ
+Mediator of RNA polymerase II transcription subunit ... , 18種, 18分子 abcdefghijklmnopqs
+Unassigned peptide ... , 6種, 6分子 rvwxyz
+非ポリマー , 3種, 20分子
+詳細
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
分子量 | 実験値: NO | ||||||||||||||||||||||||||||||||||||||||||
由来(天然) |
| ||||||||||||||||||||||||||||||||||||||||||
由来(組換発現) |
| ||||||||||||||||||||||||||||||||||||||||||
緩衝液 | pH: 7.5 | ||||||||||||||||||||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 58.56 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
-解析
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3次元再構成 | 解像度: 4.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 25967 / 対称性のタイプ: POINT |