+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6r84 | ||||||||||||
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タイトル | Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1) | ||||||||||||
要素 |
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キーワード | RIBOSOME (リボソーム) / 60S ribosomal subunit (リボソーム) / Vms1 / Arb1 / Tif6 | ||||||||||||
機能・相同性 | 機能・相同性情報 catalytic activity, acting on a tRNA / Cdc48p-Npl4p-Vms1p AAA ATPase complex / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / aminoacyl-tRNA hydrolase activity / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / maturation of 5.8S rRNA ...catalytic activity, acting on a tRNA / Cdc48p-Npl4p-Vms1p AAA ATPase complex / mitochondria-associated ubiquitin-dependent protein catabolic process / nuclear protein quality control by the ubiquitin-proteasome system / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / aminoacyl-tRNA hydrolase activity / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / maturation of 5.8S rRNA / protein quality control for misfolded or incompletely synthesized proteins / ribosomal subunit export from nucleus / SRP-dependent cotranslational protein targeting to membrane / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / ribosomal large subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / protein-RNA complex assembly / ribosomal small subunit export from nucleus / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / regulation of translational fidelity / rescue of stalled ribosome / translational termination / : / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / RNA endonuclease activity / translation initiation factor activity / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / maintenance of translational fidelity / オートファジー / modification-dependent protein catabolic process / protein tag activity / ribosomal large subunit assembly / rRNA processing / large ribosomal subunit rRNA binding / リボソーム生合成 / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / 加水分解酵素; エステル加水分解酵素 / rRNA binding / protein ubiquitination / リボソーム / structural constituent of ribosome / 翻訳 (生物学) / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / 核小体 / ATP hydrolysis activity / ミトコンドリア / RNA binding / ATP binding / metal ion binding / 細胞核 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | ||||||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) | ||||||||||||
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: 3.6 Å | ||||||||||||
データ登録者 | Su, T. / Izawa, T. / Cheng, J. / Yamashita, Y. / Berninghausen, O. / Inada, T. / Neupert, W. / Beckmann, R. | ||||||||||||
資金援助 | ドイツ, 3件
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引用 | ジャーナル: Nature / 年: 2019 タイトル: Structure and function of Vms1 and Arb1 in RQC and mitochondrial proteome homeostasis. 著者: Ting Su / Toshiaki Izawa / Matthias Thoms / Yui Yamashita / Jingdong Cheng / Otto Berninghausen / F Ulrich Hartl / Toshifumi Inada / Walter Neupert / Roland Beckmann / 要旨: Ribosome-associated quality control (RQC) provides a rescue pathway for eukaryotic cells to process faulty proteins after translational stalling of cytoplasmic ribosomes. After dissociation of ...Ribosome-associated quality control (RQC) provides a rescue pathway for eukaryotic cells to process faulty proteins after translational stalling of cytoplasmic ribosomes. After dissociation of ribosomes, the stalled tRNA-bound peptide remains associated with the 60S subunit and extended by Rqc2 by addition of C-terminal alanyl and threonyl residues (CAT tails), whereas Vms1 catalyses cleavage and release of the peptidyl-tRNA before or after addition of CAT tails. In doing so, Vms1 counteracts CAT-tailing of nuclear-encoded mitochondrial proteins that otherwise drive aggregation and compromise mitochondrial and cellular homeostasis. Here we present structural and functional insights into the interaction of Saccharomyces cerevisiae Vms1 with 60S subunits in pre- and post-peptidyl-tRNA cleavage states. Vms1 binds to 60S subunits with its Vms1-like release factor 1 (VLRF1), zinc finger and ankyrin domains. VLRF1 overlaps with the Rqc2 A-tRNA position and interacts with the ribosomal A-site, projecting its catalytic GSQ motif towards the CCA end of the tRNA, its Y285 residue dislodging the tRNA A73 for nucleolytic cleavage. Moreover, in the pre-state, we found the ABCF-type ATPase Arb1 in the ribosomal E-site, which stabilizes the delocalized A73 of the peptidyl-tRNA and stimulates Vms1-dependent tRNA cleavage. Our structural analysis provides mechanistic insights into the interplay of the RQC factors Vms1, Rqc2 and Arb1 and their role in the protection of mitochondria from the aggregation of toxic proteins. | ||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6r84.cif.gz | 3 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6r84.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 6r84.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/r8/6r84 ftp://data.pdbj.org/pub/pdb/validation_reports/r8/6r84 | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-タンパク質 , 5種, 5分子 ARXor
#1: タンパク質 | 分子量: 58604.406 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P40024 |
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#2: タンパク質 | 分子量: 48653.203 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Saccharomyces cerevisiae (パン酵母) 遺伝子: VMS1, YDR049W / 発現宿主: Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q04311 |
#3: タンパク質 | 分子量: 24156.150 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q12522 |
#16: タンパク質 | 分子量: 6032.321 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P0CH08 |
#27: タンパク質 | 分子量: 21715.035 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05317 |
+60S ribosomal protein ... , 41種, 41分子 iJjKk7lMmNnOpQ5SsTUVWPxYZabCcD...
-RNA鎖 , 4種, 4分子 34B1
#29: RNA鎖 | 分子量: 38951.105 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 1329886537 |
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#31: RNA鎖 | 分子量: 50682.922 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 1331532632 |
#34: RNA鎖 | 分子量: 24502.477 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) |
#50: RNA鎖 | 分子量: 1071848.375 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) |
-非ポリマー , 1種, 1分子
#51: 化合物 | ChemComp-ZN / |
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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 |
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分子量 | 実験値: NO | ||||||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) | 生物種: Saccharomyces cerevisiae (パン酵母) | ||||||||||||||||||||||||||||
緩衝液 | pH: 7.4 | ||||||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||
急速凍結 | 凍結剤: ETHANE |
-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: SPOT SCAN |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy |
撮影 | 電子線照射量: 2.8 e/Å2 フィルム・検出器のモデル: FEI FALCON III (4k x 4k) |
-解析
CTF補正 | タイプ: NONE |
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3次元再構成 | 解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 31832 / 対称性のタイプ: POINT |