+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-18381 | |||||||||||||||
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タイトル | UFL1 E3 ligase bound 60S ribosome | |||||||||||||||
マップデータ | DeepEMhancer map. | |||||||||||||||
試料 |
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キーワード | UFM1 / Ligase / Ribosome / Complex | |||||||||||||||
機能・相同性 | 機能・相同性情報 UFM1 ligase activity / regulation of phosphatase activity / apoptotic nuclear changes / definitive erythrocyte differentiation / UFM1 transferase activity / positive regulation of metallopeptidase activity / protein ufmylation / protein K69-linked ufmylation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to endoplasmic reticulum ...UFM1 ligase activity / regulation of phosphatase activity / apoptotic nuclear changes / definitive erythrocyte differentiation / UFM1 transferase activity / positive regulation of metallopeptidase activity / protein ufmylation / protein K69-linked ufmylation / positive regulation of RNA polymerase II regulatory region sequence-specific DNA binding / positive regulation of protein localization to endoplasmic reticulum / negative regulation of protein kinase activity by regulation of protein phosphorylation / negative regulation of IRE1-mediated unfolded protein response / regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of I-kappaB phosphorylation / positive regulation of cell cycle G1/S phase transition / protein localization to endoplasmic reticulum / regulation of intracellular estrogen receptor signaling pathway / positive regulation of proteasomal protein catabolic process / negative regulation of protein serine/threonine kinase activity / mitotic G2/M transition checkpoint / 転移酵素; アシル基を移すもの; アミノアシル基を移すもの / cartilage development / regulation of canonical NF-kappaB signal transduction / reticulophagy / mitogen-activated protein kinase binding / response to L-glutamate / regulation of neuron differentiation / regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of NF-kappaB transcription factor activity / ubiquitin-like protein ligase binding / Peptide chain elongation / mitotic G2 DNA damage checkpoint signaling / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / NF-kappaB binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / GTP hydrolysis and joining of the 60S ribosomal subunit / RHOA GTPase cycle / L13a-mediated translational silencing of Ceruloplasmin expression / hematopoietic stem cell differentiation / Major pathway of rRNA processing in the nucleolus and cytosol / endomembrane system / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / positive regulation of autophagy / cytosolic ribosome / endoplasmic reticulum unfolded protein response / positive regulation of glial cell proliferation / MDM2/MDM4 family protein binding / negative regulation of protein ubiquitination / regulation of mitotic cell cycle / response to endoplasmic reticulum stress / cyclin binding / erythrocyte differentiation / negative regulation of protein phosphorylation / liver development / negative regulation of MAP kinase activity / maturation of LSU-rRNA / DNA damage checkpoint signaling / positive regulation of protein ubiquitination / regulation of protein stability / negative regulation of protein catabolic process / brain development / Regulation of expression of SLITs and ROBOs / positive regulation of protein localization to nucleus / osteoblast differentiation / regulation of protein localization / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / response to ethanol / RNA polymerase II-specific DNA-binding transcription factor binding / mitochondrial outer membrane / cell population proliferation / cytosolic large ribosomal subunit / cytoplasmic translation / postsynaptic density / positive regulation of cell migration / structural constituent of ribosome / neuron projection / translation / negative regulation of gene expression / intracellular membrane-bounded organelle / DNA repair / focal adhesion / centrosome / DNA damage response / positive regulation of cell population proliferation / positive regulation of gene expression / endoplasmic reticulum membrane / nucleolus / negative regulation of apoptotic process / protein kinase 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: 3.2 Å | |||||||||||||||
データ登録者 | Makhlouf L / Zeqiraj E / Kulathu Y | |||||||||||||||
資金援助 | 英国, European Union, 4件
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引用 | ジャーナル: Nature / 年: 2024 タイトル: The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons. 著者: Linda Makhlouf / Joshua J Peter / Helge M Magnussen / Rohan Thakur / David Millrine / Thomas C Minshull / Grace Harrison / Joby Varghese / Frederic Lamoliatte / Martina Foglizzo / Thomas ...著者: Linda Makhlouf / Joshua J Peter / Helge M Magnussen / Rohan Thakur / David Millrine / Thomas C Minshull / Grace Harrison / Joby Varghese / Frederic Lamoliatte / Martina Foglizzo / Thomas Macartney / Antonio N Calabrese / Elton Zeqiraj / Yogesh Kulathu / 要旨: Stalled ribosomes at the endoplasmic reticulum (ER) are covalently modified with the ubiquitin-like protein UFM1 on the 60S ribosomal subunit protein RPL26 (also known as uL24). This modification, ...Stalled ribosomes at the endoplasmic reticulum (ER) are covalently modified with the ubiquitin-like protein UFM1 on the 60S ribosomal subunit protein RPL26 (also known as uL24). This modification, which is known as UFMylation, is orchestrated by the UFM1 ribosome E3 ligase (UREL) complex, comprising UFL1, UFBP1 and CDK5RAP3 (ref. ). However, the catalytic mechanism of UREL and the functional consequences of UFMylation are unclear. Here we present cryo-electron microscopy structures of UREL bound to 60S ribosomes, revealing the basis of its substrate specificity. UREL wraps around the 60S subunit to form a C-shaped clamp architecture that blocks the tRNA-binding sites at one end, and the peptide exit tunnel at the other. A UFL1 loop inserts into and remodels the peptidyl transferase centre. These features of UREL suggest a crucial function for UFMylation in the release and recycling of stalled or terminated ribosomes from the ER membrane. In the absence of functional UREL, 60S-SEC61 translocon complexes accumulate at the ER membrane, demonstrating that UFMylation is necessary for releasing SEC61 from 60S subunits. Notably, this release is facilitated by a functional switch of UREL from a 'writer' to a 'reader' module that recognizes its product-UFMylated 60S ribosomes. Collectively, we identify a fundamental role for UREL in dissociating 60S subunits from the SEC61 translocon and the basis for UFMylation in regulating protein homeostasis at the ER. | |||||||||||||||
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_18381.map.gz | 270.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-18381-v30.xml emd-18381.xml | 23.5 KB 23.5 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_18381_fsc.xml | 14.4 KB | 表示 | FSCデータファイル |
画像 | emd_18381.png | 44.9 KB | ||
マスクデータ | emd_18381_msk_1.map | 775.5 MB | マスクマップ | |
Filedesc metadata | emd-18381.cif.gz | 7.3 KB | ||
その他 | emd_18381_additional_1.map.gz emd_18381_half_map_1.map.gz emd_18381_half_map_2.map.gz | 287 MB 9 MB 9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-18381 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-18381 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_18381_validation.pdf.gz | 446 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_18381_full_validation.pdf.gz | 445.5 KB | 表示 | |
XML形式データ | emd_18381_validation.xml.gz | 27 KB | 表示 | |
CIF形式データ | emd_18381_validation.cif.gz | 34.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18381 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-18381 | HTTPS FTP |
-関連構造データ
-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_18381.map.gz / 形式: CCP4 / 大きさ: 775.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | DeepEMhancer map. | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.74 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
-マスク #1
ファイル | emd_18381_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Raw map.
ファイル | emd_18381_additional_1.map | ||||||||||||
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注釈 | Raw map. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_18381_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_18381_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : UFM1 ribosome E3 ligase complex bound to 60S ribosome
全体 | 名称: UFM1 ribosome E3 ligase complex bound to 60S ribosome |
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要素 |
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-超分子 #1: UFM1 ribosome E3 ligase complex bound to 60S ribosome
超分子 | 名称: UFM1 ribosome E3 ligase complex bound to 60S ribosome 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: 60S ribosomal protein L10a
分子 | 名称: 60S ribosomal protein L10a / 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: 24.879422 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MSSKVSRDTL YEAVREVLHG NQRKRRKFLE TVELQISLKN YDPQKDKRFS GTVRLKSTPR PKFSVCVLGD QQHCDEAKAV DIPHMDIEA LKKLNKNKKL VKKLAKKYDA FLASESLIKQ IPRILGPGLN KAGKFPSLLT HNENMVAKVD EVKSTIKFQM K KVLCLAVA ...文字列: MSSKVSRDTL YEAVREVLHG NQRKRRKFLE TVELQISLKN YDPQKDKRFS GTVRLKSTPR PKFSVCVLGD QQHCDEAKAV DIPHMDIEA LKKLNKNKKL VKKLAKKYDA FLASESLIKQ IPRILGPGLN KAGKFPSLLT HNENMVAKVD EVKSTIKFQM K KVLCLAVA VGHVKMTDDE LVYNIHLAVN FLVSLLKKNW QNVRALYIKS TMGKPQRLY UniProtKB: Large ribosomal subunit protein uL1 |
-分子 #2: E3 UFM1-protein ligase 1
分子 | 名称: E3 UFM1-protein ligase 1 / タイプ: protein_or_peptide / ID: 2 / コピー数: 1 / 光学異性体: LEVO EC番号: 転移酵素; アシル基を移すもの; アミノアシル基を移すもの |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 91.591234 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MGHHHHHHEN LYFQGMADAW EEIRRLAADF QRAQFAEATQ RLSERNCIEI VNKLIAQKQL EVVHTLDGKE YITPAQISKE MRDELHVRG GRVNIVDLQQ VINVDLIHIE NRIGDIIKSE KHVQLVLGQL IDENYLDRLA EEVNDKLQES GQVTISELCK T YDLPGNFL ...文字列: MGHHHHHHEN LYFQGMADAW EEIRRLAADF QRAQFAEATQ RLSERNCIEI VNKLIAQKQL EVVHTLDGKE YITPAQISKE MRDELHVRG GRVNIVDLQQ VINVDLIHIE NRIGDIIKSE KHVQLVLGQL IDENYLDRLA EEVNDKLQES GQVTISELCK T YDLPGNFL TQALTQRLGR IISGHIDLDN RGVIFTEAFV ARHKARIRGL FSAITRPTAV NSLISKYGFQ EQLLYSVLEE LV NSGRLRG TVVGGRQDKA VFVPDIYSRT QSTWVDSFFR QNGYLEFDAL SRLGIPDAVS YIKKRYKTTQ LLFLKAACVG QGL VDQVEA SVEEAISSGT WVDIAPLLPT SLSVEDAAIL LQQVMRAFSK QASTVVFSDT VVVSEKFIND CTELFRELMH QKAE KEMKN NPVHLITEED LKQISTLESV STSKKDKKDE RRRKATEGSG SMRGGGGGNA REYKIKKVKK KGRKDDDSDD ESQSS HTGK KKPEISFMFQ DEIEDFLRKH IQDAPEEFIS ELAEYLIKPL NKTYLEVVRS VFMSSTTSAS GTGRKRTIKD LQEEVS NLY NNIRLFEKGM KFFADDTQAA LTKHLLKSVC TDITNLIFNF LASDLMMAVD DPAAITSEIR KKILSKLSEE TKVALTK LH NSLNEKSIED FISCLDSAAE ACDIMVKRGD KKRERQILFQ HRQALAEQLK VTEDPALILH LTSVLLFQFS THSMLHAP G RCVPQIIAFL NSKIPEDQHA LLVKYQGLVV KQLVSQSKKT GQGDYPLNNE LDKEQEDVAS TTRKELQELS SSIKDLVLK SRKSSVTEE UniProtKB: E3 UFM1-protein ligase 1 |
-分子 #3: CDK5 regulatory subunit-associated protein 3
分子 | 名称: CDK5 regulatory subunit-associated protein 3 / タイプ: protein_or_peptide / ID: 3 / 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: 57.458938 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: GPLVDMEDHQ HVPIDIQTSK LLDWLVDRRH CSLKWQSLVL TIREKINAAI QDMPESEEIA QLLSGSYIHY FHCLRILDLL KGTEASTKN IFGRYSSQRM KDWQEIIALY EKDNTYLVEL SSLLVRNVNY EIPSLKKQIA KCQQLQQEYS RKEEECQAGA A EMREQFYH ...文字列: GPLVDMEDHQ HVPIDIQTSK LLDWLVDRRH CSLKWQSLVL TIREKINAAI QDMPESEEIA QLLSGSYIHY FHCLRILDLL KGTEASTKN IFGRYSSQRM KDWQEIIALY EKDNTYLVEL SSLLVRNVNY EIPSLKKQIA KCQQLQQEYS RKEEECQAGA A EMREQFYH SCKQYGITGE NVRGELLALV KDLPSQLAEI GAAAQQSLGE AIDVYQASVG FVCESPTEQV LPMLRFVQKR GN STVYEWR TGTEPSVVER PHLEELPEQV AEDAIDWGDF GVEAVSEGTD SGISAEAAGI DWGIFPESDS KDPGGDGIDW GDD AVALQI TVLEAGTQAP EGVARGPDAL TLLEYTETRN QFLDELMELE IFLAQRAVEL SEEADVLSVS QFQLAPAILQ GQTK EKMVT MVSVLEDLIG KLTSLQLQHL FMILASPRYV DRVTEFLQQK LKQSQLLALK KELMVQKQQE ALEEQAALEP KLDLL LEKT KELQKLIEAD ISKRYSGRPV NLMGTSL UniProtKB: CDK5 regulatory subunit-associated protein 3 |
-分子 #4: DDRGK domain-containing protein 1
分子 | 名称: DDRGK domain-containing protein 1 / タイプ: protein_or_peptide / ID: 4 / 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: 34.644445 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MWSHPQFEKL EVLFQGPASA GQEPLHNEEL AGAGRVAQPG PLEPEEPRAG GRPRRRRDLG SRLQAQRRAQ RVAWAEADEN EEEAVILAQ EEEGVEKPAE THLSGKIGAK KLRKLEEKQA RKAQREAEEA EREERKRLES QREAEWKKEE ERLRLEEEQK E EEERKARE ...文字列: MWSHPQFEKL EVLFQGPASA GQEPLHNEEL AGAGRVAQPG PLEPEEPRAG GRPRRRRDLG SRLQAQRRAQ RVAWAEADEN EEEAVILAQ EEEGVEKPAE THLSGKIGAK KLRKLEEKQA RKAQREAEEA EREERKRLES QREAEWKKEE ERLRLEEEQK E EEERKARE EQAQREHEEY LKLKEAFVVE EEGVGETMTE EQSQSFLTEF INYIKQSKVV LLEDLASQVG LRTQDTINRI QD LLAEGTI TGVIDDRGKF IYITPEELAA VANFIRQRGR VSIAELAQAS NSLIAWGRES PAQAPA UniProtKB: DDRGK domain-containing protein 1 |
-分子 #5: Ubiquitin-fold modifier 1
分子 | 名称: Ubiquitin-fold modifier 1 / タイプ: protein_or_peptide / ID: 5 / 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: 9.236628 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: GPGSMSKVSF KITLTSDPRL PYKVLSVPES TPFTAVLKFA AEEFKVPAAT SAIITNDGIG INPAQTAGNV FLKHGSELRI IPRDRVG UniProtKB: Ubiquitin-fold modifier 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 | 7.7 mg/mL |
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緩衝液 | pH: 7.5 / 詳細: 25 mM HEPES pH 7.5, 50 mM KCl, 5 mM MgCl2, 2 mM DTT |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: TFS Selectris X / エネルギーフィルター - スリット幅: 10 eV |
撮影 | フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) 撮影したグリッド数: 1 / 実像数: 59394 / 平均露光時間: 2.67 sec. / 平均電子線量: 33.4 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: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 0.2 µm / 倍率(公称値): 165000 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |