+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3337 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Atomic cryoEM structure of Hsp90/Cdc37/Cdk4 complex | |||||||||
マップデータ | Reconstruction of Hsp90:Cdc37:Cdk4. Part of series of maps, the highest resolution one out of the series. | |||||||||
試料 |
| |||||||||
キーワード | Hsp90 (Hsp90) / Cdc37 / Cdk4 (サイクリン依存性キナーゼ4) / chaperone (シャペロン) / kinase (キナーゼ) / unfolding | |||||||||
機能・相同性 | 機能・相同性情報 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 / regulation of type II interferon-mediated signaling pathway / Drug-mediated inhibition of CDK4/CDK6 activity ...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 / regulation of type II interferon-mediated signaling pathway / Drug-mediated inhibition of CDK4/CDK6 activity / 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 / : / very long-chain fatty acid metabolic process / HSP90-CDC37 chaperone complex / positive regulation of cyclin-dependent protein kinase activity / positive regulation of mitophagy in response to mitochondrial depolarization / Aryl hydrocarbon receptor signalling / negative regulation of proteasomal protein catabolic process / dynein axonemal particle / aryl hydrocarbon receptor complex / histone methyltransferase binding / Transcriptional regulation by RUNX2 / cellular response to phorbol 13-acetate 12-myristate / mitochondrial genome maintenance / protein kinase regulator activity / positive regulation of protein localization to cell surface / ATP-dependent protein binding / protein folding chaperone complex / negative regulation of protein metabolic process / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of tau-protein kinase activity / post-transcriptional regulation of gene expression / telomerase holoenzyme complex assembly / Uptake and function of diphtheria toxin / 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 / PTK6 Regulates Cell Cycle / positive regulation of transforming growth factor beta receptor signaling pathway / regulation of cyclin-dependent protein serine/threonine kinase activity / dendritic growth cone / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / regulation of type I interferon-mediated signaling pathway / positive regulation of phosphoprotein phosphatase activity / Sema3A PAK dependent Axon repulsion / The NLRP3 inflammasome / regulation of protein ubiquitination / HSF1-dependent transactivation / telomere maintenance via telomerase / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / response to unfolded protein / bicellular tight junction / cyclin-dependent protein kinase holoenzyme complex / HSF1 activation / protein targeting / chaperone-mediated protein complex assembly / Attenuation phase / サイクリン依存性キナーゼ / RHOBTB2 GTPase cycle / cyclin-dependent protein serine/threonine kinase activity / Purinergic signaling in leishmaniasis infection / DNA polymerase binding / supramolecular fiber organization / axonal growth cone / Signaling by ERBB2 / positive regulation of telomerase activity / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / heat shock protein binding / positive regulation of G2/M transition of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / cellular response to interleukin-4 / nitric-oxide synthase regulator activity / cyclin binding / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / placenta development / response to organic substance / Ubiquitin-dependent degradation of Cyclin D / positive regulation of cell differentiation / peptide binding / ATP-dependent protein folding chaperone / Signaling by ERBB2 TMD/JMD mutants / Hsp90 protein binding / G1/S transition of mitotic cell cycle / tau protein binding / DDX58/IFIH1-mediated induction of interferon-alpha/beta / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Oncogene Induced Senescence / Signaling by ERBB2 KD Mutants 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
データ登録者 | Verba KA / Wang RYR / Arakawa A / Liu Y / Shirouzu M / Yokoyama S / Agard DA | |||||||||
引用 | ジャーナル: Science / 年: 2016 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 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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_3337.map.gz | 59.9 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-3337-v30.xml emd-3337.xml | 16.9 KB 16.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_3337_fsc.xml | 9 KB | 表示 | FSCデータファイル |
画像 | emd_3337.tif | 118.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3337 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3337 | HTTPS FTP |
-関連構造データ
関連構造データ | 5fwkMC 3338C 3339C 3340C 3341C 3342C 3343C 3344C 5fwlC 5fwmC 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 (文献) |
---|---|
類似構造データ |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_3337.map.gz / 形式: CCP4 / 大きさ: 62.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Reconstruction of Hsp90:Cdc37:Cdk4. Part of series of maps, the highest resolution one out of the series. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.315 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-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 |
---|---|
要素 |
|
-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 |
---|---|
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 |
---|---|
由来(天然) | 生物種: Homo sapiens (ヒト) / 別称: Human / 細胞中の位置: cytoplasm |
分子量 | 理論値: 83 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) 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 |
---|---|
由来(天然) | 生物種: Homo sapiens (ヒト) / 別称: Human / 細胞中の位置: throughout |
分子量 | 理論値: 44.5 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) 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 |
---|---|
由来(天然) | 生物種: Homo sapiens (ヒト) / 別称: Human / 細胞中の位置: throughout |
分子量 | 理論値: 33.7 KDa |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) 組換プラスミド: pFastBacHT |
配列 | UniProtKB: サイクリン依存性キナーゼ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 |
---|---|
解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 0.27 mg/mL |
---|---|
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 |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: OTHER / 撮影モード: BRIGHT FIELDBright-field microscopy / 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 |
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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-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 |
---|---|
ソフトウェア | 名称: Rosetta, MDFF, Chimera, COLORES (Situs) |
詳細 | Atomic model building and refinement the Hsp90/Cdc37/Cdk4 complex was performed incrementally in five stages: 1) de novo model-building for Cdc37, 2) structure refinement of the Hsp90/Cdc37 complex, 3) de novo model extension for Cdk4 in the presence of the refined Hsp90/Cdc37 complex, and 4) structure refinement of the Hsp90/Cdc37/Cdk4 complex. The atomic structure of Hsp90/Cdc37/Cdk4 complex was used in the modelling of other low-resolution maps. |
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT / 温度因子: 95 当てはまり具合の基準: compound of Rosetta energy function and electron density fitting function |
得られたモデル | PDB-5fwk: |