+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8dp5 | ||||||||||||
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タイトル | Structure of the PEAK3/14-3-3 complex | ||||||||||||
要素 |
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キーワード | SIGNALING PROTEIN / complex / pseudokinase / kinase (キナーゼ) / adapter | ||||||||||||
機能・相同性 | 機能・相同性情報 negative regulation of peptidyl-serine dephosphorylation / regulation of heart rate by hormone / negative regulation of protein dephosphorylation / regulation of potassium ion transmembrane transporter activity / negative regulation of calcium ion transmembrane transporter activity / cytoplasmic sequestering of protein / membrane repolarization during cardiac muscle cell action potential / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of G protein-coupled receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA ...negative regulation of peptidyl-serine dephosphorylation / regulation of heart rate by hormone / negative regulation of protein dephosphorylation / regulation of potassium ion transmembrane transporter activity / negative regulation of calcium ion transmembrane transporter activity / cytoplasmic sequestering of protein / membrane repolarization during cardiac muscle cell action potential / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / negative regulation of G protein-coupled receptor signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / regulation of membrane repolarization / MTOR signalling / NADE modulates death signalling / RAB GEFs exchange GTP for GDP on RABs / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / Signaling by Hippo / vacuolar membrane / negative regulation of calcium ion export across plasma membrane / Frs2-mediated activation / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / protein kinase inhibitor activity / positive regulation of catalytic activity / cytoplasmic pattern recognition receptor signaling pathway / mTORC1-mediated signalling / regulation of heart rate by cardiac conduction / Regulation of localization of FOXO transcription factors / protein localization to nucleus / calcium channel regulator activity / phosphoserine residue binding / Regulation of HSF1-mediated heat shock response / HSF1 activation / Activation of BAD and translocation to mitochondria / potassium channel regulator activity / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / signaling adaptor activity / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of cytosolic calcium ion concentration / regulation of mitotic cell cycle / substantia nigra development / protein sequestering activity / AURKA Activation by TPX2 / positive regulation of protein export from nucleus / Translocation of SLC2A4 (GLUT4) to the plasma membrane / hippocampus development / regulation of actin cytoskeleton organization / ミトコンドリア / TP53 Regulates Metabolic Genes / phosphoprotein binding / RAF activation / neuron migration / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / cerebral cortex development / histone deacetylase binding / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / : / Regulation of PLK1 Activity at G2/M Transition / 分裂促進因子活性化タンパク質キナーゼ / Signaling by BRAF and RAF1 fusions / メラノソーム / マイクロフィラメント / MHC class II protein complex binding / cellular response to heat / regulation of cell shape / scaffold protein binding / protein phosphatase binding / transmembrane transporter binding / protein kinase activity / intracellular signal transduction / cadherin binding / protein heterodimerization activity / protein domain specific binding / focal adhesion / ubiquitin protein ligase binding / perinuclear region of cytoplasm / enzyme binding / シグナル伝達 / RNA binding / extracellular exosome / 生体膜 / identical protein binding / 細胞核 / 細胞質基質 / 細胞質 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: 3.1 Å | ||||||||||||
データ登録者 | Torosyan, H. / Paul, M. / Jura, N. / Verba, K.A. | ||||||||||||
資金援助 | 米国, 3件
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引用 | ジャーナル: Nat Commun / 年: 2023 タイトル: Structural insights into regulation of the PEAK3 pseudokinase scaffold by 14-3-3. 著者: Hayarpi Torosyan / Michael D Paul / Antoine Forget / Megan Lo / Devan Diwanji / Krzysztof Pawłowski / Nevan J Krogan / Natalia Jura / Kliment A Verba / 要旨: PEAK pseudokinases are molecular scaffolds which dimerize to regulate cell migration, morphology, and proliferation, as well as cancer progression. The mechanistic role dimerization plays in PEAK ...PEAK pseudokinases are molecular scaffolds which dimerize to regulate cell migration, morphology, and proliferation, as well as cancer progression. The mechanistic role dimerization plays in PEAK scaffolding remains unclear, as there are no structures of PEAKs in complex with their interactors. Here, we report the cryo-EM structure of dimeric PEAK3 in complex with an endogenous 14-3-3 heterodimer. Our structure reveals an asymmetric binding mode between PEAK3 and 14-3-3 stabilized by one pseudokinase domain and the SHED domain of the PEAK3 dimer. The binding interface contains a canonical phosphosite-dependent primary interaction and a unique secondary interaction not observed in previous structures of 14-3-3/client complexes. Additionally, we show that PKD regulates PEAK3/14-3-3 binding, which when prevented leads to PEAK3 nuclear enrichment and distinct protein-protein interactions. Altogether, our data demonstrate that PEAK3 dimerization forms an unusual secondary interface for 14-3-3 binding, facilitating 14-3-3 regulation of PEAK3 localization and interactome diversity. | ||||||||||||
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 | 8dp5.cif.gz | 430.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8dp5.ent.gz | 351.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8dp5.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/dp/8dp5 ftp://data.pdbj.org/pub/pdb/validation_reports/dp/8dp5 | HTTPS FTP |
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-関連構造データ
関連構造データ | 27630MC 8ds6C 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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-要素
#1: タンパク質 | 分子量: 52357.031 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PEAK3, C19orf35 / 細胞株 (発現宿主): Expi293 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q6ZS72 #2: タンパク質 | | 分子量: 28114.373 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: YWHAB / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P31946 #3: タンパク質 | | 分子量: 29208.900 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: YWHAE / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P62258 #4: タンパク質 | 分子量: 52437.012 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PEAK3, C19orf35 / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q6ZS72 構成要素の詳細 | The authors state that chains E and P are part of Chains A and B. However, because they cannot ...The authors state that chains E and P are part of Chains A and B. However, because they cannot resolve a large portion of the N-terminal segments of Chain A and B and therefore the connectivity between these two sets of chains, they cannot with confidence assign Chain E residues to Chains A or B and the same with Chain P residues. | 研究の焦点であるリガンドがあるか | N | |
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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 | 名称: Complex between PEAK3 and 14-3-3 epsilon, beta / タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT | |||||||||||||||||||||||||
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分子量 | 値: 0.1618 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: Homo sapiens (ヒト) | |||||||||||||||||||||||||
緩衝液 | pH: 7.5 詳細: A final concentration of 0.1% of Octyl-beta-Glucoside (C14H28O6) was added to the sample before freezing. | |||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 1.1 mg/ml / 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: 278.15 K / 詳細: blot time = 7s blot force = 4 |
-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 FIELDBright-field microscopy / 倍率(公称値): 105000 X / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 1000 nm / 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 | 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) / 撮影したグリッド数: 1 |
電子光学装置 | エネルギーフィルター名称: GIF Bioquantum / エネルギーフィルタースリット幅: 20 eV |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 169563 / 対称性のタイプ: POINT |