+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6o9m | ||||||
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タイトル | Structure of the human apo TFIIH | ||||||
要素 |
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キーワード | TRANSCRIPTION (転写 (生物学)) / Transcription initiation (転写 (生物学)) / Molecular dynamics (分子動力学法) / Gene regulation (遺伝子発現の調節) / Community network analysis / Global protein dynamics / RNA polymerase (RNAポリメラーゼ) | ||||||
機能・相同性 | 機能・相同性情報 MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / negative regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / ventricular system development ...MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / negative regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / ventricular system development / hair follicle maturation / cyclin-dependent protein kinase activating kinase holoenzyme complex / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / 紫外線 / CAK-ERCC2 complex / transcription factor TFIIK complex / embryonic cleavage / 5'-3' DNA helicase activity / adult heart development / G protein-coupled receptor internalization / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / nuclear thyroid hormone receptor binding / 3'-5' DNA helicase activity / 転写開始前複合体 / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / hematopoietic stem cell proliferation / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / RNA polymerase II general transcription initiation factor activity / spinal cord development / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / transcription factor TFIID complex / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / bone mineralization / erythrocyte maturation / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / ATPase activator activity / RNA Polymerase I Transcription Initiation / DNA topological change / transcription elongation by RNA polymerase I / intrinsic apoptotic signaling pathway by p53 class mediator / transcription-coupled nucleotide-excision repair / Tat-mediated elongation of the HIV-1 transcript / hematopoietic stem cell differentiation / Formation of HIV-1 elongation complex containing HIV-1 Tat / transcription by RNA polymerase I / embryonic organ development / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / response to UV / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Cyclin A:Cdk2-associated events at S phase entry / RNA Polymerase II Pre-transcription Events / DNA helicase activity / hormone-mediated signaling pathway / extracellular matrix organization / post-embryonic development / insulin-like growth factor receptor signaling pathway / transcription elongation by RNA polymerase II / chromosome segregation / determination of adult lifespan / promoter-specific chromatin binding / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase I Promoter Escape / multicellular organism growth / positive regulation of smooth muscle cell proliferation / G1/S transition of mitotic cell cycle / Dual Incision in GG-NER / NoRC negatively regulates rRNA expression / protein localization / spindle / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / cellular response to gamma radiation / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / response to calcium ion / Cyclin D associated events in G1 / protein-macromolecule adaptor activity / 4 iron, 4 sulfur cluster binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) | ||||||
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: 4.4 Å | ||||||
データ登録者 | Yan, C.L. / Dodd, T. / He, Y. / Tainer, J.A. / Tsutakawa, S.E. / Ivanov, I. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nature / 年: 2017 タイトル: The cryo-electron microscopy structure of human transcription factor IIH. 著者: Basil J Greber / Thi Hoang Duong Nguyen / Jie Fang / Pavel V Afonine / Paul D Adams / Eva Nogales / 要旨: Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcription. Composed of ten subunits ...Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcription. Composed of ten subunits that add up to a molecular mass of about 500 kDa, TFIIH is also essential for nucleotide excision repair. The seven-subunit TFIIH core complex formed by XPB, XPD, p62, p52, p44, p34, and p8 is competent for DNA repair, while the CDK-activating kinase subcomplex, which includes the kinase activity of CDK7 as well as the cyclin H and MAT1 subunits, is additionally required for transcription initiation. Mutations in the TFIIH subunits XPB, XPD, and p8 lead to severe premature ageing and cancer propensity in the genetic diseases xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy, highlighting the importance of TFIIH for cellular physiology. Here we present the cryo-electron microscopy structure of human TFIIH at 4.4 Å resolution. The structure reveals the molecular architecture of the TFIIH core complex, the detailed structures of its constituent XPB and XPD ATPases, and how the core and kinase subcomplexes of TFIIH are connected. Additionally, our structure provides insight into the conformational dynamics of TFIIH and the regulation of its activity. | ||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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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 | 6o9m.cif.gz | 574.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6o9m.ent.gz | 442.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6o9m.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/o9/6o9m ftp://data.pdbj.org/pub/pdb/validation_reports/o9/6o9m | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-TFIIH basal transcription factor complex helicase ... , 2種, 2分子 07
#1: タンパク質 | 分子量: 87021.078 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P18074, ヘリカーゼ |
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#8: タンパク質 | 分子量: 89404.734 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P19447, ヘリカーゼ |
-General transcription factor IIH subunit ... , 5種, 5分子 12456
#2: タンパク質 | 分子量: 62116.492 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P32780 |
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#3: タンパク質 | 分子量: 52245.156 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q92759 |
#5: タンパク質 | 分子量: 34416.008 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q13889 |
#6: タンパク質 | 分子量: 8060.362 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q6ZYL4 |
#7: タンパク質 | 分子量: 44481.996 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: Q13888 |
-タンパク質 , 1種, 1分子 3
#4: タンパク質 | 分子量: 35873.965 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Homo sapiens (ヒト) / 参照: UniProt: P51948 |
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-非ポリマー , 2種, 7分子
#9: 化合物 | ChemComp-SF4 / |
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#10: 化合物 | ChemComp-ZN / |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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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 | 名称: apo TFIIH / タイプ: COMPLEX / Entity ID: #1-#8 / 由来: NATURAL |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドの材料: COPPER / グリッドのタイプ: C-flat |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE |
-電子顕微鏡撮影
顕微鏡 | モデル: FEI TITAN |
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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 FIELDBright-field microscopy |
撮影 | 電子線照射量: 40 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
EMソフトウェア |
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CTF補正 | タイプ: NONE | |||||||||||||||||||||||||
3次元再構成 | 解像度: 4.4 Å / 粒子像の数: 122900 / 対称性のタイプ: POINT | |||||||||||||||||||||||||
原子モデル構築 | プロトコル: OTHER / 空間: REAL 詳細: Initial model assembled from high-resolution structures and homology models, subsequently rebuilt in COOT, refined into the Cryo-EM map using Phenix and fully validated. |