+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-21692 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
タイトル | PKA RIIbeta holoenzyme with DnaJB1-PKAc fusion in fibrolamellar hepatoceullar carcinoma | ||||||||||||
マップデータ | C1-symmetry map | ||||||||||||
試料 |
| ||||||||||||
キーワード | fibrolamellar hepatoceullar carcinoma / PKA / cAMP (CAMP) / Kinase (キナーゼ) / SIGNALING PROTEIN | ||||||||||||
機能・相同性 | 機能・相同性情報 GPER1 signaling / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 ...GPER1 signaling / PKA activation in glucagon signalling / CREB1 phosphorylation through the activation of Adenylate Cyclase / DARPP-32 events / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Factors involved in megakaryocyte development and platelet production / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / PKA activation / response to antipsychotic drug / PKA-mediated phosphorylation of CREB / PKA-mediated phosphorylation of key metabolic factors / 先体 / ROBO receptors bind AKAP5 / negative regulation of inclusion body assembly / HDL assembly / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / cAMP-dependent protein kinase regulator activity / regulation of protein binding / high-density lipoprotein particle assembly / Vasopressin regulates renal water homeostasis via Aquaporins / Rap1 signalling / nucleotide-activated protein kinase complex / renal water homeostasis / positive regulation of ATP-dependent activity / regulation of protein processing / transcription regulator inhibitor activity / protein localization to lipid droplet / regulation of bicellular tight junction assembly / cellular response to parathyroid hormone stimulus / cAMP-dependent protein kinase inhibitor activity / cell communication by electrical coupling involved in cardiac conduction / プロテインキナーゼA / cellular response to cold / Loss of phosphorylation of MECP2 at T308 / sperm capacitation / regulation of osteoblast differentiation / CREB1 phosphorylation through the activation of Adenylate Cyclase / PKA activation / cAMP-dependent protein kinase activity / negative regulation of glycolytic process through fructose-6-phosphate / ciliary base / cAMP-dependent protein kinase complex / AMP-activated protein kinase activity / postsynaptic modulation of chemical synaptic transmission / cellular response to glucagon stimulus / Triglyceride catabolism / protein kinase A regulatory subunit binding / ATPase activator activity / protein kinase A catalytic subunit binding / plasma membrane raft / chaperone cofactor-dependent protein refolding / PKA activation in glucagon signalling / : / Regulation of MECP2 expression and activity / mesoderm formation / regulation of cardiac conduction / HSF1-dependent transactivation / RET signaling / DARPP-32 events / response to unfolded protein / Interleukin-3, Interleukin-5 and GM-CSF signaling / Regulation of HSF1-mediated heat shock response / regulation of macroautophagy / sperm flagellum / regulation of cardiac muscle contraction / Attenuation phase / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / regulation of cellular response to heat / regulation of proteasomal protein catabolic process / protein kinase A signaling / protein folding chaperone / cAMP binding / forebrain development / positive regulation of gluconeogenesis / Ion homeostasis / regulation of ryanodine-sensitive calcium-release channel activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / negative regulation of TORC1 signaling / Recruitment of mitotic centrosome proteins and complexes / sperm midpiece / Hsp70 protein binding / cellular response to epinephrine stimulus / Recruitment of NuMA to mitotic centrosomes / calcium channel complex / regulation of cytosolic calcium ion concentration / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / protein export from nucleus / protein serine/threonine/tyrosine kinase activity / regulation of heart rate / CD209 (DC-SIGN) signaling 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) / Rattus norvegicus (ドブネズミ) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 7.5 Å | ||||||||||||
データ登録者 | Lu T-W / Aoto PC | ||||||||||||
資金援助 | 米国, 3件
| ||||||||||||
引用 | ジャーナル: PLoS Biol / 年: 2020 タイトル: Structural analyses of the PKA RIIβ holoenzyme containing the oncogenic DnaJB1-PKAc fusion protein reveal protomer asymmetry and fusion-induced allosteric perturbations in ...タイトル: Structural analyses of the PKA RIIβ holoenzyme containing the oncogenic DnaJB1-PKAc fusion protein reveal protomer asymmetry and fusion-induced allosteric perturbations in fibrolamellar hepatocellular carcinoma. 著者: Tsan-Wen Lu / Phillip C Aoto / Jui-Hung Weng / Cole Nielsen / Jennifer N Cash / James Hall / Ping Zhang / Sanford M Simon / Michael A Cianfrocco / Susan S Taylor / 要旨: When the J-domain of the heat shock protein DnaJB1 is fused to the catalytic (C) subunit of cAMP-dependent protein kinase (PKA), replacing exon 1, this fusion protein, J-C subunit (J-C), becomes the ...When the J-domain of the heat shock protein DnaJB1 is fused to the catalytic (C) subunit of cAMP-dependent protein kinase (PKA), replacing exon 1, this fusion protein, J-C subunit (J-C), becomes the driver of fibrolamellar hepatocellular carcinoma (FL-HCC). Here, we use cryo-electron microscopy (cryo-EM) to characterize J-C bound to RIIβ, the major PKA regulatory (R) subunit in liver, thus reporting the first cryo-EM structure of any PKA holoenzyme. We report several differences in both structure and dynamics that could not be captured by the conventional crystallography approaches used to obtain prior structures. Most striking is the asymmetry caused by the absence of the second cyclic nucleotide binding (CNB) domain and the J-domain in one of the RIIβ:J-C protomers. Using molecular dynamics (MD) simulations, we discovered that this asymmetry is already present in the wild-type (WT) RIIβ2C2 but had been masked in the previous crystal structure. This asymmetry may link to the intrinsic allosteric regulation of all PKA holoenzymes and could also explain why most disease mutations in PKA regulatory subunits are dominant negative. The cryo-EM structure, combined with small-angle X-ray scattering (SAXS), also allowed us to predict the general position of the Dimerization/Docking (D/D) domain, which is essential for localization and interacting with membrane-anchored A-Kinase-Anchoring Proteins (AKAPs). This position provides a multivalent mechanism for interaction of the RIIβ holoenzyme with membranes and would be perturbed in the oncogenic fusion protein. The J-domain also alters several biochemical properties of the RIIβ holoenzyme: It is easier to activate with cAMP, and the cooperativity is reduced. These results provide new insights into how the finely tuned allosteric PKA signaling network is disrupted by the oncogenic J-C subunit, ultimately leading to the development of FL-HCC. | ||||||||||||
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_21692.map.gz | 40.3 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-21692-v30.xml emd-21692.xml | 13.1 KB 13.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_21692.png | 40.3 KB | ||
Filedesc metadata | emd-21692.cif.gz | 5.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-21692 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21692 | HTTPS FTP |
-関連構造データ
-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_21692.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | C1-symmetry map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1 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 : PKA RIIbeta holoenzyme with DnaJB1-PKAc fusion in fibrolamellar h...
全体 | 名称: PKA RIIbeta holoenzyme with DnaJB1-PKAc fusion in fibrolamellar hepatoceullar carcinoma |
---|---|
要素 |
|
-超分子 #1: PKA RIIbeta holoenzyme with DnaJB1-PKAc fusion in fibrolamellar h...
超分子 | 名称: PKA RIIbeta holoenzyme with DnaJB1-PKAc fusion in fibrolamellar hepatoceullar carcinoma タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
---|
-超分子 #2: DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase c...
超分子 | 名称: DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha fusion タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1 |
---|---|
由来(天然) | 生物種: Homo sapiens (ヒト) |
-超分子 #3: cAMP-dependent protein kinase type II-beta regulatory subunit
超分子 | 名称: cAMP-dependent protein kinase type II-beta regulatory subunit タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #2 |
---|---|
由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) |
-分子 #1: DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase c...
分子 | 名称: DnaJ homolog subfamily B member 1,cAMP-dependent protein kinase catalytic subunit alpha fusion タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO / EC番号: プロテインキナーゼA |
---|---|
由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 47.337984 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: GKDYYQTLGL ARGASDEEIK RAYRRQALRY HPDKNKEPGA EEKFKEIAEA YDVLSDPRKR EIFDRYGEEV KEFLAKAKED FLKKWESPA QNTAHLDQFE RIKTLGTGSF GRVMLVKHKE TGNHYAMKIL DKQKVVKLKQ IEHTLNEKRI LQAVNFPFLV K LEFSFKDN ...文字列: GKDYYQTLGL ARGASDEEIK RAYRRQALRY HPDKNKEPGA EEKFKEIAEA YDVLSDPRKR EIFDRYGEEV KEFLAKAKED FLKKWESPA QNTAHLDQFE RIKTLGTGSF GRVMLVKHKE TGNHYAMKIL DKQKVVKLKQ IEHTLNEKRI LQAVNFPFLV K LEFSFKDN SNLYMVMEYV PGGEMFSHLR RIGRFSEPHA RFYAAQIVLT FEYLHSLDLI YRDLKPENLL IDQQGYIQVT DF GFAKRVK GRTWTLCGTP EYLAPEIILS KGYNKGVDWW ALGVLIYEMA AGYPPFFADQ PIQIYEKIVS GKVRFPSHFS SDL KDLLRN LLQVDLTKRF GNLKNGVNDI KNHKWFATTD WIAIYQRKVE APFIPKFKGP GDTSNFDDYE EEEIRVSINE KCGK EFSEF UniProtKB: DnaJ homolog subfamily B member 1, cAMP-dependent protein kinase catalytic subunit alpha |
-分子 #2: cAMP-dependent protein kinase type II-beta regulatory subunit
分子 | 名称: cAMP-dependent protein kinase type II-beta regulatory subunit タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO |
---|---|
由来(天然) | 生物種: Rattus norvegicus (ドブネズミ) |
分子量 | 理論値: 46.177852 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MSIEIPAGLT ELLQGFTVEV LRHQPADLLE FALQHFTRLQ QENERKGAAR FGHEGRTWGD AGAAAGGGTP SKGVNFAEEP MRSDSENGE EEEAAEAGAF NAPVINRFTR RASVCAEAYN PDEEEDDAES RIIHPKTDDQ RNRLQEACKD ILLFKNLDPE Q MSQVLDAM ...文字列: MSIEIPAGLT ELLQGFTVEV LRHQPADLLE FALQHFTRLQ QENERKGAAR FGHEGRTWGD AGAAAGGGTP SKGVNFAEEP MRSDSENGE EEEAAEAGAF NAPVINRFTR RASVCAEAYN PDEEEDDAES RIIHPKTDDQ RNRLQEACKD ILLFKNLDPE Q MSQVLDAM FEKLVKEGEH VIDQGDDGDN FYVIDRGTFD IYVKCDGVGR CVGNYDNRGS FGELALMYNT PRAATITATS PG ALWGLDR VTFRRIIVKN NAKKRKMYES FIESLPFLKS LEVSERLKVV DVIGTKVYND GEQIIAQGDS ADSFFIVESG EVR ITMKRK GKSDIEENGA VEIARCLRGQ YFGELALVTN KPRAASAHAI GTVKCLAMDV QAFERLLGPC MEIMKRNIAT YEEQ LVALF GTNMDIVEPT A UniProtKB: cAMP-dependent protein kinase type II-beta regulatory subunit |
-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
緩衝液 | pH: 5.8 |
---|---|
凍結 | 凍結剤: ETHANE |
-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: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: COUNTING / 平均電子線量: 80.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: OTHER / 詳細: Stochastic gradient descent |
---|---|
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 7.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 11182 |