+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-25363 | ||||||||||||
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タイトル | The structure of the PP2A-B56gamma1 holoenzyme-PME-1 complex | ||||||||||||
マップデータ | |||||||||||||
試料 |
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キーワード | The structure of PP2A-B56gamma holoenzyme-PME-1 complex / RECOMBINATION | ||||||||||||
機能・相同性 | 機能・相同性情報 protein phosphatase methylesterase-1 / protein C-terminal methylesterase activity / protein methylesterase activity / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / regulation of meiotic cell cycle process involved in oocyte maturation / mitotic sister chromatid separation ...protein phosphatase methylesterase-1 / protein C-terminal methylesterase activity / protein methylesterase activity / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / regulation of meiotic cell cycle process involved in oocyte maturation / mitotic sister chromatid separation / protein serine/threonine phosphatase complex / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / FAR/SIN/STRIPAK complex / protein demethylation / positive regulation of microtubule binding / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / female meiotic nuclear division / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / protein antigen binding / protein phosphatase regulator activity / GABA receptor binding / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Initiation of Nuclear Envelope (NE) Reformation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / ERKs are inactivated / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / lncRNA binding / negative regulation of epithelial to mesenchymal transition / protein phosphatase inhibitor activity / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / protein serine/threonine phosphatase activity / Platelet sensitization by LDL / CTLA4 inhibitory signaling / myosin phosphatase activity / protein-serine/threonine phosphatase / regulation of cell differentiation / T cell homeostasis / ERK/MAPK targets / protein phosphatase activator activity / mesoderm development / regulation of G1/S transition of mitotic cell cycle / phosphoprotein phosphatase activity / DARPP-32 events / chromosome, centromeric region / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of hippo signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / 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 / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Resolution of Sister Chromatid Cohesion / protein dephosphorylation / AURKA Activation by TPX2 / protein tyrosine phosphatase activity / protein phosphatase 2A binding / meiotic cell cycle / chromosome segregation / RHO GTPases Activate Formins / response to lead ion / RAF activation / regulation of protein phosphorylation / Spry regulation of FGF signaling / positive regulation of protein serine/threonine kinase activity / Degradation of beta-catenin by the destruction complex / tau protein binding / PKR-mediated signaling / spindle pole / Negative regulation of MAPK pathway / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / Regulation of TP53 Degradation / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / protein-containing complex assembly / protein phosphatase binding 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: 3.4 Å | ||||||||||||
データ登録者 | Li Y / Balakrishnan VK | ||||||||||||
資金援助 | 3件
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引用 | ジャーナル: Elife / 年: 2022 タイトル: Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition. 著者: Yitong Li / Vijaya Kumar Balakrishnan / Michael Rowse / Cheng-Guo Wu / Anastasia Phoebe Bravos / Vikash K Yadav / Ylva Ivarsson / Stefan Strack / Irina V Novikova / Yongna Xing / 要旨: Protein phosphatase 2A (PP2A) holoenzymes target broad substrates by recognizing short motifs via regulatory subunits. PP2A methylesterase 1 (PME-1) is a cancer-promoting enzyme and undergoes ...Protein phosphatase 2A (PP2A) holoenzymes target broad substrates by recognizing short motifs via regulatory subunits. PP2A methylesterase 1 (PME-1) is a cancer-promoting enzyme and undergoes methylesterase activation upon binding to the PP2A core enzyme. Here, we showed that PME-1 readily demethylates different families of PP2A holoenzymes and blocks substrate recognition in vitro. The high-resolution cryoelectron microscopy structure of a PP2A-B56 holoenzyme-PME-1 complex reveals that PME-1 disordered regions, including a substrate-mimicking motif, tether to the B56 regulatory subunit at remote sites. They occupy the holoenzyme substrate-binding groove and allow large structural shifts in both holoenzyme and PME-1 to enable multipartite contacts at structured cores to activate the methylesterase. B56 interface mutations selectively block PME-1 activity toward PP2A-B56 holoenzymes and affect the methylation of a fraction of total cellular PP2A. The B56 interface mutations allow us to uncover B56-specific PME-1 functions in p53 signaling. Our studies reveal multiple mechanisms of PME-1 in suppressing holoenzyme functions and versatile PME-1 activities derived from coupling substrate-mimicking motifs to dynamic structured cores. #1: ジャーナル: Acta Crystallogr., Sect. D: Biol. Crystallogr. 年: 2018 タイトル: Real-space refinement in PHENIX for cryo-EM and crystallography 著者: Xing Y | ||||||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_25363.map.gz | 217.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-25363-v30.xml emd-25363.xml | 15.6 KB 15.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_25363.png | 39.6 KB | ||
Filedesc metadata | emd-25363.cif.gz | 6.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-25363 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25363 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_25363_validation.pdf.gz | 436.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_25363_full_validation.pdf.gz | 435.7 KB | 表示 | |
XML形式データ | emd_25363_validation.xml.gz | 7.8 KB | 表示 | |
CIF形式データ | emd_25363_validation.cif.gz | 9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25363 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25363 | HTTPS FTP |
-関連構造データ
関連構造データ | 7soyMC 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) |
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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
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「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_25363.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.53 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-試料の構成要素
-全体 : The structure of PP2A-B56gamma holoenzyme-PME-1 complex
全体 | 名称: The structure of PP2A-B56gamma holoenzyme-PME-1 complex |
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要素 |
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-超分子 #1: The structure of PP2A-B56gamma holoenzyme-PME-1 complex
超分子 | 名称: The structure of PP2A-B56gamma holoenzyme-PME-1 complex タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-分子 #1: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit...
分子 | 名称: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 65.378344 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MAAADGDDSL YPIAVLIDEL RNEDVQLRLN SIKKLSTIAL ALGVERTRSE LLPFLTDTIY DEDEVLLALA EQLGTFTTLV GGPEYVHCL LPPLESLATV EETVVRDKAV ESLRAISHEH SPSDLEAHFV PLVKRLAGGD WFTSRTSACG LFSVCYPRVS S AVKAELRQ ...文字列: MAAADGDDSL YPIAVLIDEL RNEDVQLRLN SIKKLSTIAL ALGVERTRSE LLPFLTDTIY DEDEVLLALA EQLGTFTTLV GGPEYVHCL LPPLESLATV EETVVRDKAV ESLRAISHEH SPSDLEAHFV PLVKRLAGGD WFTSRTSACG LFSVCYPRVS S AVKAELRQ YFRNLCSDDT PMVRRAAASK LGEFAKVLEL DNVKSEIIPM FSNLASDEQD SVRLLAVEAC VNIAQLLPQE DL EALVMPT LRQAAEDKSW RVRYMVADKF TELQKAVGPE ITKTDLVPAF QNLMKDCEAE VRAAASHKVK EFCENLSADC REN VIMSQI LPCIKELVSD ANQHVKSALA SVIMGLSPIL GKDNTIEHLL PLFLAQLKDE CPEVRLNIIS NLDCVNEVIG IRQL SQSLL PAIVELAEDA KWRVRLAIIE YMPLLAGQLG VEFFDEKLNS LCMAWLVDHV YAIREAATSN LKKLVEKFGK EWAHA TIIP KVLAMSGDPN YLHRMTTLFC INVLSEVCGQ DITTKHMLPT VLRMAGDPVA NVRFNVAKSL QKIGPILDNS TLQSEV KPI LEKLTQDQDV DVKYFAQEAL TVLSLA UniProtKB: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform |
-分子 #2: Isoform Gamma-1 of Serine/threonine-protein phosphatase 2A 56 kDa...
分子 | 名称: Isoform Gamma-1 of Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 52.69527 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MLTCNKAGSR MVVDAANSNG PFQPVVLLHI RDVPPADQEK LFIQKLRQCC VLFDFVSDPL SDLKWKEVKR AALSEMVEYI THNRNVITE PIYPEVVHMF AVNMFRTLPP SSNPTGAEFD PEEDEPTLEA AWPHLQLVYE FFLRFLESPD FQPNIAKKYI D QKFVLQLL ...文字列: MLTCNKAGSR MVVDAANSNG PFQPVVLLHI RDVPPADQEK LFIQKLRQCC VLFDFVSDPL SDLKWKEVKR AALSEMVEYI THNRNVITE PIYPEVVHMF AVNMFRTLPP SSNPTGAEFD PEEDEPTLEA AWPHLQLVYE FFLRFLESPD FQPNIAKKYI D QKFVLQLL ELFDSEDPRE RDFLKTTLHR IYGKFLGLRA YIRKQINNIF YRFIYETEHH NGIAELLEIL GSIINGFALP LK EEHKIFL LKVLLPLHKV KSLSVYHPQL AYCVVQFLEK DSTLTEPVVM ALLKYWPKTH SPKEVMFLNE LEEILDVIEP SEF VKIMEP LFRQLAKCVS SPHFQVAERA LYYWNNEYIM SLISDNAAKI LPIMFPSLYR NSKTHWNKTI HGLIYNALKL FMEM NQKLF DDCTQQFKAE KLKEKLKMKE REEAWVKIEN LAKANPQVLK KRIT UniProtKB: Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform |
-分子 #3: Serine/threonine-protein phosphatase 2A catalytic subunit alpha i...
分子 | 名称: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform タイプ: protein_or_peptide / ID: 3 / コピー数: 1 / 光学異性体: LEVO / EC番号: protein-serine/threonine phosphatase |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 35.636152 KDa |
組換発現 | 生物種: Trichoplusia ni (イラクサキンウワバ) |
配列 | 文字列: MDEKVFTKEL DQWIEQLNEC KQLSESQVKS LCEKAKEILT KESNVQEVRC PVTVCGDVHG QFHDLMELFR IGGKSPDTNY LFMGDYVDR GYYSVETVTL LVALKVRYRE RITILRGNHE SRQITQVYGF YDECLRKYGN ANVWKYFTDL FDYLPLTALV D GQIFCLHG ...文字列: MDEKVFTKEL DQWIEQLNEC KQLSESQVKS LCEKAKEILT KESNVQEVRC PVTVCGDVHG QFHDLMELFR IGGKSPDTNY LFMGDYVDR GYYSVETVTL LVALKVRYRE RITILRGNHE SRQITQVYGF YDECLRKYGN ANVWKYFTDL FDYLPLTALV D GQIFCLHG GLSPSIDTLD HIRALDRLQE VPHEGPMCDL LWSDPDDRGG WGISPRGAGY TFGQDISETF NHANGLTLVS RA HQLVMEG YNWCHDRNVV TIFSAPNYCY RCGNQAAIME LDDTLKYSFL QFDPAPRRGE PHVTRRTPDY FL UniProtKB: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform |
-分子 #4: Protein phosphatase methylesterase 1
分子 | 名称: Protein phosphatase methylesterase 1 / タイプ: protein_or_peptide / ID: 4 / コピー数: 1 / 光学異性体: LEVO / EC番号: protein phosphatase methylesterase-1 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 42.352379 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MSALEKSMHL GRLPSRPPLP GSGGSQSGAK MRMGPGRKRD FSPVPWSQYF ESMEDVEVEN ETGKDTFRVY KSGSEGPVLL LLHGGGHSA LSWAVFTAAI ISRVQCRIVA LDLRSHGETK VKNPEDLSAE TMAKDVGNVV EAMYGDLPPP IMLIGHAMGG A IAVHTASS ...文字列: MSALEKSMHL GRLPSRPPLP GSGGSQSGAK MRMGPGRKRD FSPVPWSQYF ESMEDVEVEN ETGKDTFRVY KSGSEGPVLL LLHGGGHSA LSWAVFTAAI ISRVQCRIVA LDLRSHGETK VKNPEDLSAE TMAKDVGNVV EAMYGDLPPP IMLIGHAMGG A IAVHTASS NLVPSLLGLC MIDVVEGTAM DALNSMQNFL RGRPKTFKSL ENAIEWSVKS GQIRNLESAR VSMVGQVKQC EG ITSPEGS KSIVEGIIEE EEEDEEGSES ISKRKKEDDM ETKKDHPYTW RIELAKTEKY WDGWFRGLSN LFLSCPIPKL LLL AGVDRL DKDLTIGQMQ GKFQMQVLPQ CGHAVHEDAP DKVAEAVATF LIRHRFAEPI GGFQCVFPGC UniProtKB: Protein phosphatase methylesterase 1 |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 1 mg/mL |
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緩衝液 | pH: 8 |
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 300 / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 50.8 e/Å2 |
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 FIELD 最大 デフォーカス(公称値): 2.3000000000000003 µm 最小 デフォーカス(公称値): 1.5 µm |
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: Ab initio model generated by cryoSparc |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 276737 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |