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基本情報
登録情報 | データベース: EMDB / ID: EMD-3342 | |||||||||
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タイトル | Atomic cryoEM structure of Hsp90/Cdc37/Cdk4 complex | |||||||||
![]() | Reconstruction of Hsp90:Cdc37:Cdk4 complex. Part of series of maps, the highest resolution map being EMD-3337. This is a different subclass from the same particles as in EMD-3337, having well defined Cdk4 N-Lobe. Other relevant maps are EMD-3338, EMD-3339, EMD-3340, EMD-3341 | |||||||||
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![]() | Hsp90 / Cdc37 / Cdk4 / chaperone / kinase / unfolding | |||||||||
機能・相同性 | ![]() cyclin D3-CDK4 complex / cyclin D1-CDK4 complex / cyclin D2-CDK4 complex / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 / cellular response to ionomycin / citrulline metabolic process / regulation of transcription initiation by RNA polymerase II / Drug-mediated inhibition of CDK4/CDK6 activity / regulation of type II interferon-mediated signaling pathway ...cyclin D3-CDK4 complex / cyclin D1-CDK4 complex / cyclin D2-CDK4 complex / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 / cellular response to ionomycin / citrulline metabolic process / regulation of transcription initiation by RNA polymerase II / Drug-mediated inhibition of CDK4/CDK6 activity / regulation of type II interferon-mediated signaling pathway / Evasion of Oncogene Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / Evasion of Oxidative Stress Induced Senescence Due to Defective p16INK4A binding to CDK4 and CDK6 / regulation of type B pancreatic cell proliferation / receptor ligand inhibitor activity / PTK6 Regulates Cell Cycle / very long-chain fatty acid metabolic process / HSP90-CDC37 chaperone complex / positive regulation of mitophagy in response to mitochondrial depolarization / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / aryl hydrocarbon receptor complex / dynein axonemal particle / histone methyltransferase binding / cellular response to phorbol 13-acetate 12-myristate / Transcriptional regulation by RUNX2 / mitochondrial genome maintenance / positive regulation of protein localization to cell surface / ATP-dependent protein binding / cyclin-dependent kinase / protein kinase regulator activity / cyclin-dependent protein serine/threonine kinase activity / protein folding chaperone complex / cyclin-dependent protein serine/threonine kinase regulator activity / post-transcriptional regulation of gene expression / telomerase holoenzyme complex assembly / Respiratory syncytial virus genome replication / Uptake and function of diphtheria toxin / regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of G2/M transition of mitotic cell cycle / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / TPR domain binding / positive regulation of transforming growth factor beta receptor signaling pathway / Assembly and release of respiratory syncytial virus (RSV) virions / cyclin-dependent protein kinase holoenzyme complex / regulation of G2/M transition of mitotic cell cycle / dendritic growth cone / regulation of type I interferon-mediated signaling pathway / : / : / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / The NLRP3 inflammasome / Signaling by ERBB2 / telomere maintenance via telomerase / HSF1-dependent transactivation / cyclin binding / response to unfolded protein / chaperone-mediated protein complex assembly / HSF1 activation / bicellular tight junction / Attenuation phase / protein targeting / cellular response to interleukin-4 / RHOBTB2 GTPase cycle / axonal growth cone / Purinergic signaling in leishmaniasis infection / DNA polymerase binding / supramolecular fiber organization / chaperone-mediated protein folding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding chaperone / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / nitric-oxide synthase regulator activity / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / Signaling by ERBB2 TMD/JMD mutants / Meiotic recombination / peptide binding / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Ubiquitin-dependent degradation of Cyclin D / Signaling by ERBB2 KD Mutants / placenta development / positive regulation of cell differentiation / Transcriptional regulation of granulopoiesis / SCF(Skp2)-mediated degradation of p27/p21 / ATP-dependent protein folding chaperone / kinase binding / Downregulation of ERBB2 signaling 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 8.0 Å | |||||||||
![]() | Verba KA / Wang RYR / Arakawa A / Liu Y / Shirouzu M / Yokoyama S / Agard DA | |||||||||
![]() | ![]() タイトル: Atomic structure of Hsp90-Cdc37-Cdk4 reveals that Hsp90 traps and stabilizes an unfolded kinase. 著者: Kliment A Verba / Ray Yu-Ruei Wang / Akihiko Arakawa / Yanxin Liu / Mikako Shirouzu / Shigeyuki Yokoyama / David A Agard / ![]() ![]() 要旨: The Hsp90 molecular chaperone and its Cdc37 cochaperone help stabilize and activate more than half of the human kinome. However, both the mechanism by which these chaperones assist their "client" ...The Hsp90 molecular chaperone and its Cdc37 cochaperone help stabilize and activate more than half of the human kinome. However, both the mechanism by which these chaperones assist their "client" kinases and the reason why some kinases are addicted to Hsp90 while closely related family members are independent are unknown. Our structural understanding of these interactions is lacking, as no full-length structures of human Hsp90, Cdc37, or either of these proteins with a kinase have been elucidated. Here we report a 3.9 angstrom cryo-electron microscopy structure of the Hsp90-Cdc37-Cdk4 kinase complex. Surprisingly, the two lobes of Cdk4 are completely separated with the β4-β5 sheet unfolded. Cdc37 mimics part of the kinase N lobe, stabilizing an open kinase conformation by wedging itself between the two lobes. Finally, Hsp90 clamps around the unfolded kinase β5 strand and interacts with exposed N- and C-lobe interfaces, protecting the kinase in a trapped unfolded state. On the basis of this structure and an extensive amount of previously collected data, we propose unifying conceptual and mechanistic models of chaperone-kinase interactions. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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マップデータ | ![]() | 59.7 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 17 KB 17 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 10.7 KB | 表示 | ![]() |
画像 | ![]() | 128.1 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 5fwmMC ![]() 3337C ![]() 3338C ![]() 3339C ![]() 3340C ![]() 3341C ![]() 3343C ![]() 3344C ![]() 5fwkC ![]() 5fwlC ![]() 5fwpC 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 ( |
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類似構造データ |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of Hsp90:Cdc37:Cdk4 complex. Part of series of maps, the highest resolution map being EMD-3337. This is a different subclass from the same particles as in EMD-3337, having well defined Cdk4 N-Lobe. Other relevant maps are EMD-3338, EMD-3339, EMD-3340, EMD-3341 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.315 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
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試料の構成要素
-全体 : Complex of Human Hsp90 beta, human Cdc37 and human Cdk4
全体 | 名称: Complex of Human Hsp90 beta, human Cdc37 and human Cdk4 |
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要素 |
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-超分子 #1000: Complex of Human Hsp90 beta, human Cdc37 and human Cdk4
超分子 | 名称: Complex of Human Hsp90 beta, human Cdc37 and human Cdk4 タイプ: sample / ID: 1000 / 詳細: All three proteins were co-expressed in Sf9 cells. 集合状態: One Hsp90 homodimer binds to one Cdc37 and one Cdk4 Number unique components: 3 |
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分子量 | 実験値: 245 KDa / 理論値: 245 KDa / 手法: As cloned, verified by SDS-PAGE |
-分子 #1: Heat Shock Protein HSP 90 beta
分子 | 名称: Heat Shock Protein HSP 90 beta / タイプ: protein_or_peptide / ID: 1 / Name.synonym: Hsp90 / コピー数: 2 / 集合状態: Dimer / 組換発現: Yes |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 83 KDa |
組換発現 | 生物種: ![]() ![]() 組換プラスミド: pFastBacHT |
配列 | UniProtKB: Heat shock protein HSP 90-beta / GO: citrulline metabolic process / InterPro: Heat shock protein Hsp90 family |
-分子 #2: Hsp90 co-chaperone Cdc37
分子 | 名称: Hsp90 co-chaperone Cdc37 / タイプ: protein_or_peptide / ID: 2 / Name.synonym: Cdc37 / コピー数: 1 / 組換発現: Yes |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 44.5 KDa |
組換発現 | 生物種: ![]() ![]() 組換プラスミド: pFastBacHT |
配列 | UniProtKB: Hsp90 co-chaperone Cdc37 / GO: mitochondrial genome maintenance |
-分子 #3: Cyclin-dependent kinase 4
分子 | 名称: Cyclin-dependent kinase 4 / タイプ: protein_or_peptide / ID: 3 / Name.synonym: Cdk4 / コピー数: 1 / 組換発現: Yes |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 33.7 KDa |
組換発現 | 生物種: ![]() ![]() 組換プラスミド: pFastBacHT |
配列 | UniProtKB: Cyclin-dependent kinase 4 / GO: very long-chain fatty acid metabolic process / InterPro: Protein kinase domain |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 0.27 mg/mL |
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緩衝液 | pH: 7.5 詳細: 20mM Tris-HCl (pH 7.5), 150 mM NaCl, 10 mM KCl, 10 mM MgCl2, 20 mM Na2MoO4, 2mM DTT, 0.085mM DDM |
グリッド | 詳細: Glow discharged for 30 sec, C-flat 400 mesh 1.2/1.3 thick carbon grids (Protochips) |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / チャンバー内温度: 95 K / 装置: FEI VITROBOT MARK III / 手法: Single blot from 4 to 6 seconds, at 20C |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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アライメント法 | Legacy - 非点収差: At high mag via FT. |
日付 | 2014年11月25日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 実像数: 3718 / 平均電子線量: 44 e/Å2 / 詳細: 38 frames, 7.6 seconds total exposure / ビット/ピクセル: 8 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: OTHER / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 3.8 µm / 最小 デフォーカス(公称値): 1.4 µm / 倍率(公称値): 22500 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
-原子モデル構築 1
初期モデル | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: E / Chain - #3 - Chain ID: K |
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ソフトウェア | 名称: Chimera, Rosetta |
詳細 | Residues 5-85 (N-lobe) of Cdk4 from 3G33 were fit in Chimera as rigid body into EMD-3342. Such fit N-lobe of Cdk4 was further tweaked in Coot in the context of 5FWK to join the Cdk4 chain and minimize clashes for each of the maps. To relieve atomic clashes or bond length/angle distortions at the linker regions, these models were subjected to "Cartesian space relax" protocol within corresponding density maps using Rosetta. Final models were selected using the combined score of Rosetta all-atom physically-realistic score and electron density score. |
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT / 温度因子: 130 当てはまり具合の基準: cross correlation of fit into the density with Rosetta force field score |
得られたモデル | ![]() PDB-5fwm: |