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万見- EMDB-16908: 60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native) -
+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-16908 | ||||||||||||||||||
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タイトル | 60S ribosomal subunit bound to the E3-UFM1 complex - state 1 (native) | ||||||||||||||||||
マップデータ | |||||||||||||||||||
試料 |
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キーワード | ER / UFMylation / recycling / RIBOSOME | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 UFM1 ligase activity / positive regulation of reticulophagy / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / epidermal growth factor binding / endoplasmic reticulum Sec complex / negative regulation of IRE1-mediated unfolded protein response / pronephric nephron development / endoplasmic reticulum quality control compartment ...UFM1 ligase activity / positive regulation of reticulophagy / UFM1 transferase activity / protein ufmylation / protein K69-linked ufmylation / epidermal growth factor binding / endoplasmic reticulum Sec complex / negative regulation of IRE1-mediated unfolded protein response / pronephric nephron development / endoplasmic reticulum quality control compartment / regulation of proteasomal ubiquitin-dependent protein catabolic process / cotranslational protein targeting to membrane / Ssh1 translocon complex / lamin filament / Sec61 translocon complex / negative regulation of T cell mediated immune response to tumor cell / regulation of fatty acid biosynthetic process / protein targeting to ER / regulation of megakaryocyte differentiation / protein insertion into ER membrane / negative regulation of T cell activation / miRNA-mediated post-transcriptional gene silencing / regulation of intracellular estrogen receptor signaling pathway / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / SRP-dependent cotranslational protein targeting to membrane, translocation / 90S preribosome assembly / signal sequence binding / post-translational protein targeting to membrane, translocation / ribosome disassembly / TORC2 complex binding / 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 / GAIT complex / middle ear morphogenesis / regulation of canonical NF-kappaB signal transduction / regulation of reactive oxygen species metabolic process / regulation of glycolytic process / A band / reticulophagy / cytoplasmic side of rough endoplasmic reticulum membrane / alpha-beta T cell differentiation / regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / response to L-glutamate / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / retrograde protein transport, ER to cytosol / optic nerve development / negative regulation of ubiquitin protein ligase activity / negative regulation of NF-kappaB transcription factor activity / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / response to aldosterone / retinal ganglion cell axon guidance / G1 to G0 transition / homeostatic process / maturation of 5.8S rRNA / macrophage chemotaxis / lung morphogenesis / male meiosis I / Protein hydroxylation / ribosomal large subunit binding / Peptide chain elongation / positive regulation of glial cell proliferation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / blastocyst development / preribosome, large subunit precursor / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / protein transmembrane transporter activity / Viral mRNA Translation / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / hematopoietic stem cell differentiation / L13a-mediated translational silencing of Ceruloplasmin expression / protein-RNA complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / cellular response to interleukin-4 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal subunit export from nucleus / ossification / cellular response to actinomycin D / positive regulation of autophagy / ERAD pathway / cytosolic ribosome / rough endoplasmic reticulum / Maturation of protein E 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: 3.3 Å | ||||||||||||||||||
データ登録者 | Penchev I / DaRosa PA / Becker T / Beckmann R / Kopito R | ||||||||||||||||||
資金援助 | European Union, ドイツ, 英国, 米国, 5件
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引用 | ジャーナル: Nature / 年: 2024 タイトル: UFM1 E3 ligase promotes recycling of 60S ribosomal subunits from the ER. 著者: Paul A DaRosa / Ivan Penchev / Samantha C Gumbin / Francesco Scavone / Magda Wąchalska / Joao A Paulo / Alban Ordureau / Joshua J Peter / Yogesh Kulathu / J Wade Harper / Thomas Becker / ...著者: Paul A DaRosa / Ivan Penchev / Samantha C Gumbin / Francesco Scavone / Magda Wąchalska / Joao A Paulo / Alban Ordureau / Joshua J Peter / Yogesh Kulathu / J Wade Harper / Thomas Becker / Roland Beckmann / Ron R Kopito / 要旨: Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour. UFM1 is a UBL that ...Reversible modification of target proteins by ubiquitin and ubiquitin-like proteins (UBLs) is widely used by eukaryotic cells to control protein fate and cell behaviour. UFM1 is a UBL that predominantly modifies a single lysine residue on a single ribosomal protein, uL24 (also called RPL26), on ribosomes at the cytoplasmic surface of the endoplasmic reticulum (ER). UFM1 conjugation (UFMylation) facilitates the rescue of 60S ribosomal subunits (60S) that are released after ribosome-associated quality-control-mediated splitting of ribosomes that stall during co-translational translocation of secretory proteins into the ER. Neither the molecular mechanism by which the UFMylation machinery achieves such precise target selection nor how this ribosomal modification promotes 60S rescue is known. Here we show that ribosome UFMylation in vivo occurs on free 60S and we present sequential cryo-electron microscopy snapshots of the heterotrimeric UFM1 E3 ligase (E3(UFM1)) engaging its substrate uL24. E3(UFM1) binds the L1 stalk, empty transfer RNA-binding sites and the peptidyl transferase centre through carboxy-terminal domains of UFL1, which results in uL24 modification more than 150 Å away. After catalysing UFM1 transfer, E3(UFM1) remains stably bound to its product, UFMylated 60S, forming a C-shaped clamp that extends all the way around the 60S from the transfer RNA-binding sites to the polypeptide tunnel exit. Our structural and biochemical analyses suggest a role for E3(UFM1) in post-termination release and recycling of the large ribosomal subunit from the ER membrane. | ||||||||||||||||||
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_16908.map.gz | 484.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-16908-v30.xml emd-16908.xml | 78.1 KB 78.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_16908.png | 75.7 KB | ||
Filedesc metadata | emd-16908.cif.gz | 15.8 KB | ||
その他 | emd_16908_half_map_1.map.gz emd_16908_half_map_2.map.gz | 487 MB 486.9 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-16908 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16908 | 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_16908.map.gz / 形式: CCP4 / 大きさ: 600.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 0.727 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
-ハーフマップ: #1
ファイル | emd_16908_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: #2
ファイル | emd_16908_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 : 60S ribosomal subunit in complex with E3-UFM1 ligase, State 1
+超分子 #1: 60S ribosomal subunit in complex with E3-UFM1 ligase, State 1
+超分子 #2: 60S ribosomal subunit
+超分子 #3: E3 UFM1-protein ligase 1
+分子 #1: Protein transport protein Sec61 subunit alpha isoform 1
+分子 #2: Protein transport protein Sec61 subunit gamma
+分子 #3: Protein transport protein Sec61 subunit beta
+分子 #7: E3 UFM1-protein ligase 1
+分子 #8: Eukaryotic translation initiation factor 6
+分子 #9: 60S ribosomal protein L8
+分子 #10: 60S ribosomal protein L3
+分子 #11: 60S ribosomal protein L4
+分子 #12: 60S ribosomal protein L5
+分子 #13: 60S ribosomal protein L6
+分子 #14: 60S ribosomal protein L7
+分子 #15: 60S ribosomal protein L7a
+分子 #16: 60S ribosomal protein L9
+分子 #17: Ribosomal protein uL16-like
+分子 #18: 60S ribosomal protein L11
+分子 #19: 60S ribosomal protein L13
+分子 #20: 60S ribosomal protein L14
+分子 #21: 60S ribosomal protein L15
+分子 #22: 60S ribosomal protein L13a
+分子 #23: 60S ribosomal protein L17
+分子 #24: 60S ribosomal protein L18
+分子 #25: 60S ribosomal protein L19
+分子 #26: 60S ribosomal protein L18a
+分子 #27: 60S ribosomal protein L21
+分子 #28: 60S ribosomal protein L22
+分子 #29: 60S ribosomal protein L23
+分子 #30: 60S ribosomal protein L24
+分子 #31: 60S ribosomal protein L23a
+分子 #32: 60S ribosomal protein L26
+分子 #33: 60S ribosomal protein L27
+分子 #34: 60S ribosomal protein L27a
+分子 #35: 60S ribosomal protein L29
+分子 #36: 60S ribosomal protein L30
+分子 #37: 60S ribosomal protein L31
+分子 #38: 60S ribosomal protein L32
+分子 #39: 60S ribosomal protein L35a
+分子 #40: 60S ribosomal protein L34
+分子 #41: 60S ribosomal protein L35
+分子 #42: 60S ribosomal protein L36
+分子 #43: 60S ribosomal protein L37
+分子 #44: 60S ribosomal protein L38
+分子 #45: 60S ribosomal protein L39
+分子 #46: Ubiquitin-60S ribosomal protein L40
+分子 #47: 60S ribosomal protein L36a
+分子 #48: 60S ribosomal protein L37a
+分子 #49: 60S ribosomal protein L28
+分子 #50: 60S ribosomal protein L10a
+分子 #4: 28S rRNA
+分子 #5: 5S rRNA
+分子 #6: 5.8S rRNA
+分子 #51: MAGNESIUM ION
+分子 #52: ZINC ION
-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
緩衝液 | pH: 7.5 |
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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: FEI FALCON IV (4k x 4k) 平均電子線量: 60.0 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): 3.0 µm / 最小 デフォーカス(公称値): 0.5 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 |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 20750 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |