+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0452 | |||||||||||||||
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タイトル | Cryo-EM structure of the human TFIIH core complex | |||||||||||||||
マップデータ | Sharpened and low-pass filtered cryo-EM map. | |||||||||||||||
試料 |
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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 / 3'-5' DNA helicase activity / nuclear thyroid hormone receptor binding / 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 / spinal cord development / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / bone mineralization / 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 / erythrocyte maturation / regulation of cyclin-dependent protein serine/threonine kinase activity / ATPase activator activity / regulation of G1/S transition of mitotic cell cycle / RNA Polymerase I Transcription Initiation / transcription elongation by RNA polymerase I / DNA topological change / intrinsic apoptotic signaling pathway by p53 class mediator / transcription-coupled nucleotide-excision repair / hematopoietic stem cell differentiation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / embryonic organ development / transcription by RNA polymerase I / Formation of HIV elongation complex in the absence of HIV Tat / Cyclin E associated events during G1/S transition / RNA Polymerase II Transcription Elongation / Cyclin A/B1/B2 associated events during G2/M transition / Formation of RNA Pol II elongation complex / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to UV / 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 / chromosome segregation / determination of adult lifespan / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / positive regulation of smooth muscle cell proliferation / G1/S transition of mitotic cell cycle / multicellular organism growth / cellular response to gamma radiation / NoRC negatively regulates rRNA expression / protein localization / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / spindle / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / response to calcium ion / Gap-filling DNA repair synthesis and ligation in TC-NER / Cyclin D associated events in G1 / protein-macromolecule adaptor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / 4 iron, 4 sulfur cluster binding 類似検索 - 分子機能 | |||||||||||||||
生物種 | Homo sapiens (ヒト) / Human (ヒト) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.7 Å | |||||||||||||||
データ登録者 | Greber BJ / Toso D / Fang J / Nogales E | |||||||||||||||
資金援助 | 米国, スイス, 4件
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引用 | ジャーナル: Elife / 年: 2019 タイトル: The complete structure of the human TFIIH core complex. 著者: Basil J Greber / Daniel B Toso / Jie Fang / Eva Nogales / 要旨: Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is ...Transcription factor IIH (TFIIH) is a heterodecameric protein complex critical for transcription initiation by RNA polymerase II and nucleotide excision DNA repair. The TFIIH core complex is sufficient for its repair functions and harbors the XPB and XPD DNA-dependent ATPase/helicase subunits, which are affected by human disease mutations. Transcription initiation additionally requires the CdK activating kinase subcomplex. Previous structural work has provided only partial insight into the architecture of TFIIH and its interactions within transcription pre-initiation complexes. Here, we present the complete structure of the human TFIIH core complex, determined by phase-plate cryo-electron microscopy at 3.7 Å resolution. The structure uncovers the molecular basis of TFIIH assembly, revealing how the recruitment of XPB by p52 depends on a pseudo-symmetric dimer of homologous domains in these two proteins. The structure also suggests a function for p62 in the regulation of XPD, and allows the mapping of previously unresolved human disease mutations. | |||||||||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_0452.map.gz | 59.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0452-v30.xml emd-0452.xml | 31.2 KB 31.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_0452.png | 166 KB | ||
その他 | emd_0452_half_map_1.map.gz emd_0452_half_map_2.map.gz | 49.7 MB 49.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0452 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0452 | HTTPS FTP |
-関連構造データ
関連構造データ | 6nmiMC 0587C 0588C 0589C 0602C 0603C 0604C 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 | |
電子顕微鏡画像生データ | EMPIAR-10430 (タイトル: Phase-plate cryo-EM of human TFIIH / Data size: 9.2 TB Data #1: Unaligned movies of human TFIIH, using the Volta phase plate, dataset 1 [micrographs - multiframe] Data #2: Unaligned movies of human TFIIH, using the Volta phase plate, dataset 2 [micrographs - multiframe] Data #3: Unaligned movies of human TFIIH, using the Volta phase plate, dataset 3 [micrographs - multiframe] Data #4: Unaligned movies of human TFIIH, using the Volta phase plate, dataset 4 [micrographs - multiframe] Data #5: Unaligned movies of human TFIIH, using the Volta phase plate, dataset 5 [micrographs - multiframe] Data #6: Unaligned movies of human TFIIH, using the Volta phase plate, dataset 6 [micrographs - multiframe]) |
-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_0452.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Sharpened and low-pass filtered cryo-EM map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-ハーフマップ: Unfiltered half-map.
ファイル | emd_0452_half_map_1.map | ||||||||||||
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注釈 | Unfiltered half-map. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Unfiltered half-map.
ファイル | emd_0452_half_map_2.map | ||||||||||||
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注釈 | Unfiltered half-map. | ||||||||||||
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 : Transcription factor IIH (TFIIH)
+超分子 #1: Transcription factor IIH (TFIIH)
+分子 #1: General transcription and DNA repair factor IIH helicase subunit XPB
+分子 #2: General transcription and DNA repair factor IIH helicase subunit XPD
+分子 #3: General transcription factor IIH subunit 1, p62
+分子 #4: General transcription factor IIH subunit 4, p52
+分子 #5: General transcription factor IIH subunit 2, p44
+分子 #6: General transcription factor IIH subunit 3, p34
+分子 #7: General transcription factor IIH subunit 5, p8
+分子 #8: CDK-activating kinase assembly factor MAT1
+分子 #9: IRON/SULFUR CLUSTER
+分子 #10: ZINC 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 | 0.0049 mg/mL | ||||||||||||||
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緩衝液 | pH: 7.9 構成要素:
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グリッド | モデル: C-flat / 材質: COPPER / メッシュ: 400 / 支持フィルム - #0 - Film type ID: 1 / 支持フィルム - #0 - 材質: CARBON / 支持フィルム - #0 - トポロジー: HOLEY / 支持フィルム - #1 - Film type ID: 2 / 支持フィルム - #1 - 材質: CARBON / 支持フィルム - #1 - トポロジー: CONTINUOUS / 前処理 - タイプ: PLASMA CLEANING / 詳細: Gatan Solarus | ||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV 詳細: A thin film of continuous carbon was floated onto Protochips C-flat CF-4/2 holey carbon grids and glow discharged or plasma cleaned before application of 4 uL of sample solution.. |
-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 | 倍率(補正後): 43478 / 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): 0.7 µm / 最小 デフォーカス(公称値): 0.5 µm |
特殊光学系 | 位相板: VOLTA PHASE PLATE / エネルギーフィルター - 名称: GIF Quantum LS / エネルギーフィルター - スリット幅: 20 eV |
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 |
詳細 | Residual beam tilt corrected in RELION 3. |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 撮影したグリッド数: 7 / 実像数: 21437 / 平均露光時間: 8.25 sec. / 平均電子線量: 50.0 e/Å2 詳細: Images were collected as dose-fractionated movie frames (33 or 50 frames per exposure). |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
CTF補正 | ソフトウェア:
詳細: CTF correction during 3D reconstruction in RELION 3. | ||||||
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初期モデル | モデルのタイプ: EMDB MAP EMDB ID: | ||||||
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3) | ||||||
最終 3次元分類 | クラス数: 8 / 平均メンバー数/クラス: 100000 / ソフトウェア - 名称: RELION (ver. 3) | ||||||
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD / ソフトウェア - 名称: RELION (ver. 3) | ||||||
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: FOURIER SPACE / 解像度のタイプ: BY AUTHOR / 解像度: 3.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 3) / 使用した粒子像数: 138659 |
-原子モデル構築 1
初期モデル | (PDB ID: , , , , , , ) |
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詳細 | Reference structures and homology models were docked and subsequently completely rebuilt according to the density. Parts of the structure were traced de novo. |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
得られたモデル | PDB-6nmi: |