+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7b5q | ||||||
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タイトル | Cryo-EM structure of the human CAK bound to ICEC0942 (PHENIX-OPLS3e) | ||||||
要素 |
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キーワード | TRANSCRIPTION / Kinase / protein complex / small molecules inhibitor / CDK-activating kinase | ||||||
機能・相同性 | 機能・相同性情報 ventricular system development / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / adult heart development / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity ...ventricular system development / snRNA transcription by RNA polymerase II / CAK-ERCC2 complex / transcription factor TFIIK complex / adult heart development / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / [RNA-polymerase]-subunit kinase / RNA Polymerase I Transcription Termination / cyclin-dependent protein serine/threonine kinase regulator activity / Cyclin E associated events during G1/S transition / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / Cyclin A/B1/B2 associated events during G2/M transition / 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 / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / RNA polymerase II CTD heptapeptide repeat kinase activity / regulation of G1/S transition of mitotic cell cycle / RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ATP-dependent activity, acting on DNA / Formation of HIV elongation complex in the absence of HIV Tat / male germ cell nucleus / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / positive regulation of smooth muscle cell proliferation / RNA Polymerase I Promoter Escape / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / NoRC negatively regulates rRNA expression / response to calcium ion / Cyclin D associated events in G1 / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / G1/S transition of mitotic cell cycle / Formation of TC-NER Pre-Incision Complex / fibrillar center / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / RUNX1 regulates transcription of genes involved in differentiation of HSCs / transcription by RNA polymerase II / protein stabilization / regulation of cell cycle / protein kinase activity / cell division / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol 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: 2.5 Å | ||||||
データ登録者 | Greber, B.J. / Remis, J. / Ali, S. / Nogales, E. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Biophys J / 年: 2021 タイトル: 2.5 Å-resolution structure of human CDK-activating kinase bound to the clinical inhibitor ICEC0942. 著者: Basil J Greber / Jonathan Remis / Simak Ali / Eva Nogales / 要旨: The human CDK-activating kinase (CAK), composed of CDK7, cyclin H, and MAT1, is involved in the control of transcription initiation and the cell cycle. Because of these activities, it has been ...The human CDK-activating kinase (CAK), composed of CDK7, cyclin H, and MAT1, is involved in the control of transcription initiation and the cell cycle. Because of these activities, it has been identified as a promising target for cancer chemotherapy. A number of CDK7 inhibitors have entered clinical trials, among them ICEC0942 (also known as CT7001). Structural information can aid in improving the affinity and specificity of such drugs or drug candidates, reducing side effects in patients. Here, we have determined the structure of the human CAK in complex with ICEC0942 at 2.5 Å-resolution using cryogenic electron microscopy. Our structure reveals conformational differences of ICEC0942 compared with previous X-ray crystal structures of the CDK2-bound complex, and highlights the critical ability of cryogenic electron microscopy to resolve structures of drug-bound protein complexes without the need to crystalize the protein target. | ||||||
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 | 7b5q.cif.gz | 242 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7b5q.ent.gz | 190 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7b5q.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 | 7b5q_validation.pdf.gz | 1.3 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7b5q_full_validation.pdf.gz | 1.3 MB | 表示 | |
XML形式データ | 7b5q_validation.xml.gz | 29.4 KB | 表示 | |
CIF形式データ | 7b5q_validation.cif.gz | 42.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/b5/7b5q ftp://data.pdbj.org/pub/pdb/validation_reports/b5/7b5q | HTTPS FTP |
-関連構造データ
関連構造データ | 12042MC 7b5oC C: 同じ文献を引用 (文献) M: このデータのモデリングに利用したマップデータ |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10561 (タイトル: Cryo-EM structure of the human CDK-activating kinase bound to the clinical inhibitor ICEC0942 Data size: 3.8 TB Data #1: Unaligned movies of human CAK-ICEC0942, dataset 1 [micrographs - multiframe] Data #2: Unaligned movies of human CAK-ICEC0942, dataset 3 [micrographs - multiframe] Data #3: Unaligned movies of human CAK-ICEC0942, dataset 2 [micrographs - multiframe]) |
実験データセット #1 | データ参照: 10.6019/EMPIAR-10561 / データの種類: EMPIAR |
-リンク
-集合体
登録構造単位 |
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-要素
#1: タンパク質 | 分子量: 38132.340 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: MNAT1, CAP35, MAT1, RNF66 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P51948 |
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#2: タンパク質 | 分子量: 37695.473 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CCNH / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P51946 |
#3: タンパク質 | 分子量: 43651.070 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CDK7, CAK, CAK1, CDKN7, MO15, STK1 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) 参照: UniProt: P50613, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase |
#4: 化合物 | ChemComp-I74 / ( |
#5: 水 | ChemComp-HOH / |
研究の焦点であるリガンドがあるか | Y |
-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: CDK-activating kinase bound to ICEC0942 / タイプ: COMPLEX / Entity ID: #1-#3 / 由来: RECOMBINANT | ||||||||||||||||||||||||||||||
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分子量 | 値: 0.12 MDa / 実験値: NO | ||||||||||||||||||||||||||||||
由来(天然) | 生物種: Homo sapiens (ヒト) | ||||||||||||||||||||||||||||||
由来(組換発現) | 生物種: Trichoplusia ni (イラクサキンウワバ) | ||||||||||||||||||||||||||||||
緩衝液 | pH: 7.9 | ||||||||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.2 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: Incubated with 50 uM ICEC0942 for 5 min | ||||||||||||||||||||||||||||||
試料支持 | グリッドの材料: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: UltrAuFoil R1.2/1.3 | ||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE-PROPANE / 湿度: 100 % / 凍結前の試料温度: 278 K |
-電子顕微鏡撮影
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company | ||||||||||||
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顕微鏡 | モデル: FEI TALOS ARCTICA | ||||||||||||
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM | ||||||||||||
電子レンズ | モード: BRIGHT FIELD / 倍率(補正後): 72886 X / 最大 デフォーカス(公称値): 1500 nm / 最小 デフォーカス(公称値): 500 nm / Cs: 2.7 mm / C2レンズ絞り径: 50 µm / アライメント法: COMA FREE | ||||||||||||
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER | ||||||||||||
撮影 | Imaging-ID: 1 / 平均露光時間: 2 sec. / 電子線照射量: 69 e/Å2 / フィルム・検出器のモデル: GATAN K3 (6k x 4k)
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-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 10904715 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 2.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 205478 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 2 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL 詳細: Real space refinement in PHENIX combined with the OPLS3e force field (Schrodinger 2020-3). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 6XBZ Accession code: 6XBZ / Source name: PDB / タイプ: experimental model |