+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8gae | |||||||||||||||
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タイトル | Hsp90 provides platform for CRaf dephosphorylation by PP5 | |||||||||||||||
要素 |
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キーワード | CHAPERONE / kinase / phosphatase / complex | |||||||||||||||
機能・相同性 | 機能・相同性情報 regulation of type II interferon-mediated signaling pathway / response to arachidonate / receptor ligand inhibitor activity / HSP90-CDC37 chaperone complex / death-inducing signaling complex assembly / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / peptidyl-serine dephosphorylation / : / peptidyl-threonine dephosphorylation ...regulation of type II interferon-mediated signaling pathway / response to arachidonate / receptor ligand inhibitor activity / HSP90-CDC37 chaperone complex / death-inducing signaling complex assembly / negative regulation of proteasomal protein catabolic process / Aryl hydrocarbon receptor signalling / peptidyl-serine dephosphorylation / : / peptidyl-threonine dephosphorylation / aryl hydrocarbon receptor complex / intermediate filament cytoskeleton organization / dynein axonemal particle / regulation of Rho protein signal transduction / histone methyltransferase binding / type B pancreatic cell proliferation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / positive regulation of protein localization to cell surface / ATP-dependent protein binding / Rap1 signalling / regulation of cell motility / protein kinase regulator activity / insulin secretion involved in cellular response to glucose stimulus / protein folding chaperone complex / response to morphine / Negative feedback regulation of MAPK pathway / post-transcriptional regulation of gene expression / telomerase holoenzyme complex assembly / Respiratory syncytial virus genome replication / Uptake and function of diphtheria toxin / GP1b-IX-V activation signalling / protein serine/threonine phosphatase activity / activation of adenylate cyclase activity / regulation of cyclin-dependent protein serine/threonine kinase activity / IFNG signaling activates MAPKs / 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 / myosin phosphatase activity / TPR domain binding / protein-serine/threonine phosphatase / regulation of cell differentiation / ERBB2-ERBB3 signaling pathway / Assembly and release of respiratory syncytial virus (RSV) virions / positive regulation of transforming growth factor beta receptor signaling pathway / pseudopodium / face development / dendritic growth cone / somatic stem cell population maintenance / phosphatase activity / regulation of type I interferon-mediated signaling pathway / : / The NLRP3 inflammasome / neurotrophin TRK receptor signaling pathway / phosphoprotein phosphatase activity / thyroid gland development / Sema3A PAK dependent Axon repulsion / regulation of protein ubiquitination / telomere maintenance via telomerase / HSF1-dependent transactivation / response to unfolded protein / extrinsic apoptotic signaling pathway via death domain receptors / chaperone-mediated protein complex assembly / MAP kinase kinase kinase activity / HSF1 activation / Attenuation phase / type II interferon-mediated signaling pathway / RHOBTB2 GTPase cycle / protein targeting / Purinergic signaling in leishmaniasis infection / cellular response to interleukin-4 / negative regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / axonal growth cone / Schwann cell development / DNA polymerase binding / supramolecular fiber organization / chaperone-mediated protein folding / Signaling by ERBB2 / heat shock protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein folding chaperone / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to muscle stretch / nitric-oxide synthase regulator activity / myelination / protein dephosphorylation / CD209 (DC-SIGN) signaling / Constitutive Signaling by Overexpressed ERBB2 / ESR-mediated signaling / : / insulin-like growth factor receptor signaling pathway 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: 3.3 Å | |||||||||||||||
データ登録者 | Jaime-Garza, M. / Nowotny, C.A. / Coutandin, D. / Wang, F. / Tabios, M. / Agard, D.A. | |||||||||||||||
資金援助 | 米国, 4件
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引用 | ジャーナル: Nat Commun / 年: 2023 タイトル: Hsp90 provides a platform for kinase dephosphorylation by PP5. 著者: Maru Jaime-Garza / Carlos A Nowotny / Daniel Coutandin / Feng Wang / Mariano Tabios / David A Agard / 要旨: The Hsp90 molecular chaperone collaborates with the phosphorylated Cdc37 cochaperone for the folding and activation of its many client kinases. As with many kinases, the Hsp90 client kinase CRaf is ...The Hsp90 molecular chaperone collaborates with the phosphorylated Cdc37 cochaperone for the folding and activation of its many client kinases. As with many kinases, the Hsp90 client kinase CRaf is activated by phosphorylation at specific regulatory sites. The cochaperone phosphatase PP5 dephosphorylates CRaf and Cdc37 in an Hsp90-dependent manner. Although dephosphorylating Cdc37 has been proposed as a mechanism for releasing Hsp90-bound kinases, here we show that Hsp90 bound kinases sterically inhibit Cdc37 dephosphorylation indicating kinase release must occur before Cdc37 dephosphorylation. Our cryo-EM structure of PP5 in complex with Hsp90:Cdc37:CRaf reveals how Hsp90 both activates PP5 and scaffolds its association with the bound CRaf to dephosphorylate phosphorylation sites neighboring the kinase domain. Thus, we directly show how Hsp90's role in maintaining protein homeostasis goes beyond folding and activation to include post translationally modifying its client kinases. | |||||||||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8gae.cif.gz | 740.5 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8gae.ent.gz | 614.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8gae.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 | 8gae_validation.pdf.gz | 1.2 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8gae_full_validation.pdf.gz | 1.3 MB | 表示 | |
XML形式データ | 8gae_validation.xml.gz | 70.6 KB | 表示 | |
CIF形式データ | 8gae_validation.cif.gz | 106.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ga/8gae ftp://data.pdbj.org/pub/pdb/validation_reports/ga/8gae | HTTPS FTP |
-関連構造データ
関連構造データ | 29895MC 8gftC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-タンパク質 , 4種, 5分子 ABCDE
#1: タンパク質 | 分子量: 83595.484 Da / 分子数: 2 / 由来タイプ: 組換発現 詳細: Sequence starts with HRV 3C cleavage site, followed by human Hsp90B sequence. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: HSP90AB1, HSP90B, HSPC2, HSPCB / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 株 (発現宿主): JEL-1 / 参照: UniProt: P08238 #2: タンパク質 | | 分子量: 45352.223 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: CDC37, CDC37A / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 株 (発現宿主): JEL-1 / 参照: UniProt: Q16543 #3: タンパク質 | | 分子量: 23841.605 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: RAF1, RAF / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 株 (発現宿主): JEL-1 参照: UniProt: P04049, non-specific serine/threonine protein kinase #4: タンパク質 | | 分子量: 57184.730 Da / 分子数: 1 / Mutation: H304A / 由来タイプ: 組換発現 詳細: Sequence starts with HRV 3C cleavage site, continued by human PP5 sequence. 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PPP5C, PPP5 / 発現宿主: Escherichia coli BL21 (大腸菌) 参照: UniProt: P53041, protein-serine/threonine phosphatase |
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-非ポリマー , 5種, 8分子
#5: 化合物 | #6: 化合物 | #7: 化合物 | ChemComp-ADP / | #8: 化合物 | ChemComp-ATP / | #9: 化合物 | |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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-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 |
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分子量 |
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由来(天然) |
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由来(組換発現) |
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緩衝液 | pH: 7.5 | ||||||||||||||||||||||||||||||
緩衝液成分 |
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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: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 283.15 K 詳細: 3UL OF SAMPLE 10C 100% HUMIDITY 30S WAIT TIME 3S BLOT TIME -2 BLOT FORCE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
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 FIELD / 倍率(公称値): 105000 X / 最大 デフォーカス(公称値): 1800 nm / 最小 デフォーカス(公称値): 800 nm |
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 | 電子線照射量: 69 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 実像数: 4160 |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / 分類: 精密化 | ||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 3730385 / 詳細: Gaussian blob particle picking in cryoSPARC. | ||||||||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 522000 / アルゴリズム: FOURIER SPACE 詳細: Three different maps were used for final composite map: Hsp90:Cdc37: 288k particles, 3.2A PP5 TPR: 215k particles, 3.3A PP5 catalytic domain and CRaf kinase C-lobe: 22k particles, 4.0A ...詳細: Three different maps were used for final composite map: Hsp90:Cdc37: 288k particles, 3.2A PP5 TPR: 215k particles, 3.3A PP5 catalytic domain and CRaf kinase C-lobe: 22k particles, 4.0A Composite half maps were used to get the final resolution in Relion PostProcessing. All original maps provided in the "Related entries" tab. クラス平均像の数: 3 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT 詳細: This model was built using rigid body docking in Chimera and ChimeraX for all main chains, and RosettaCM to add remaining fragments not included in previous models. Refinement was done using ...詳細: This model was built using rigid body docking in Chimera and ChimeraX for all main chains, and RosettaCM to add remaining fragments not included in previous models. Refinement was done using iterative Phenix and RosettaRelax, and finalized with ISOLDE. | ||||||||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 |
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精密化 | 最高解像度: 3.3 Å |