+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-30170 | |||||||||
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タイトル | Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4delta63-87 strain at 3.12 Angstroms resolution(state R1) | |||||||||
マップデータ | Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4%u220663-87 strain at 3.12 Angstroms resolution(state R1) | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / 7S RNA binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / hexon binding / pre-mRNA 5'-splice site binding / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / SRP-dependent cotranslational protein targeting to membrane ...protein-RNA complex remodeling / regulation of ribosomal subunit export from nucleus / 7S RNA binding / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / hexon binding / pre-mRNA 5'-splice site binding / maturation of 5.8S rRNA / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 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) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / ATPase activator activity / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / nuclear-transcribed mRNA catabolic process / translational elongation / ribosomal large subunit export from nucleus / regulation of translational fidelity / protein-RNA complex assembly / ribosomal subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / translation initiation factor activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / nuclear periphery / assembly of large subunit precursor of preribosome / maturation of SSU-rRNA / cytosolic ribosome assembly / small-subunit processome / macroautophagy / maintenance of translational fidelity / rRNA processing / ribosome biogenesis / viral capsid / ribosomal large subunit assembly / ATPase binding / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / structural constituent of ribosome / translation / GTPase activity / mRNA binding / GTP binding / host cell nucleus / nucleolus / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae S288C (パン酵母) / Baker's yeast (パン酵母) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.12 Å | |||||||||
データ登録者 | Li Y / Wilson DM | |||||||||
資金援助 | 米国, 中国, 2件
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引用 | ジャーナル: Nat Commun / 年: 2020 タイトル: Structural insights into assembly of the ribosomal nascent polypeptide exit tunnel. 著者: Daniel M Wilson / Yu Li / Amber LaPeruta / Michael Gamalinda / Ning Gao / John L Woolford / 要旨: The nascent polypeptide exit tunnel (NPET) is a major functional center of 60S ribosomal subunits. However, little is known about how the NPET is constructed during ribosome assembly. We utilized ...The nascent polypeptide exit tunnel (NPET) is a major functional center of 60S ribosomal subunits. However, little is known about how the NPET is constructed during ribosome assembly. We utilized molecular genetics, biochemistry, and cryo-electron microscopy (cryo-EM) to investigate the functions of two NPET-associated proteins, ribosomal protein uL4 and assembly factor Nog1, in NPET assembly. Structures of mutant pre-ribosomes lacking the tunnel domain of uL4 reveal a misassembled NPET, including an aberrantly flexible ribosomal RNA helix 74, resulting in at least three different blocks in 60S assembly. Structures of pre-ribosomes lacking the C-terminal extension of Nog1 demonstrate that this extension scaffolds the tunnel domain of uL4 in the NPET to help maintain stability in the core of pre-60S subunits. Our data reveal that uL4 and Nog1 work together in the maturation of ribosomal RNA helix 74, which is required to ensure proper construction of the NPET and 60S ribosomal subunits. | |||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_30170.map.gz | 96.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-30170-v30.xml emd-30170.xml | 57.1 KB 57.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_30170.png | 65.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-30170 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30170 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_30170_validation.pdf.gz | 577 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_30170_full_validation.pdf.gz | 576.5 KB | 表示 | |
XML形式データ | emd_30170_validation.xml.gz | 6.5 KB | 表示 | |
CIF形式データ | emd_30170_validation.cif.gz | 7.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30170 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30170 | 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_30170.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-EM structure of pre-60S ribosome from Saccharomyces cerevisiae rpl4%u220663-87 strain at 3.12 Angstroms resolution(state R1) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.3734 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
+全体 : Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisi...
+超分子 #1: Eukaryotic pre-60S ribosomal subunits from Saccharomyces cerevisi...
+分子 #1: 60S ribosomal protein L2-A
+分子 #2: 60S ribosomal protein L3
+分子 #3: 60S ribosomal protein L4-A
+分子 #4: 60S ribosomal protein L5
+分子 #5: 60S ribosomal protein L6-A
+分子 #6: 60S ribosomal protein L7-A
+分子 #7: 60S ribosomal protein L8-A
+分子 #8: 60S ribosomal protein L9-A
+分子 #9: 60S ribosomal protein L11-A
+分子 #10: 60S ribosomal protein L13-A
+分子 #11: 60S ribosomal protein L14-A
+分子 #12: 60S ribosomal protein L15-A
+分子 #13: 60S ribosomal protein L16-A
+分子 #14: 60S ribosomal protein L17-A
+分子 #15: 60S ribosomal protein L18-A
+分子 #16: 60S ribosomal protein L19-A
+分子 #17: 60S ribosomal protein L20-A
+分子 #18: 60S ribosomal protein L21-A
+分子 #19: 60S ribosomal protein L22-A
+分子 #20: 60S ribosomal protein L23-A
+分子 #21: Ribosome assembly factor MRT4
+分子 #22: 60S ribosomal protein L25
+分子 #23: 60S ribosomal protein L26-A
+分子 #24: 60S ribosomal protein L27-A
+分子 #25: 60S ribosomal protein L28
+分子 #26: Nucleolar GTP-binding protein 1
+分子 #27: 60S ribosomal protein L30
+分子 #28: 60S ribosomal protein L31-A
+分子 #29: 60S ribosomal protein L32
+分子 #30: 60S ribosomal protein L33-A
+分子 #31: 60S ribosomal protein L34-A
+分子 #32: 60S ribosomal protein L35-A
+分子 #33: 60S ribosomal protein L36-A
+分子 #34: 60S ribosomal protein L37-A
+分子 #35: 60S ribosomal protein L38
+分子 #36: Nucleolar GTP-binding protein 2
+分子 #37: 60S ribosomal protein L43-A
+分子 #38: Ribosome biogenesis protein NSA2
+分子 #39: Ribosome biogenesis protein RLP24
+分子 #40: Ribosome biogenesis protein RPF2
+分子 #41: Regulator of ribosome biosynthesis
+分子 #42: Ribosome assembly protein 4
+分子 #43: Eukaryotic translation initiation factor 6
+分子 #44: UPF0642 protein YBL028C
+分子 #45: RDN25-1 rRNA
+分子 #46: RDN5.8-1 rRNA
+分子 #47: RDN5-2 rRNA
+分子 #48: GUANOSINE-5'-TRIPHOSPHATE
+分子 #49: MAGNESIUM ION
+分子 #50: 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: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 1.9 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: SPOT SCAN / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.12 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 103319 |
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初期 角度割当 | タイプ: ANGULAR RECONSTITUTION |
最終 角度割当 | タイプ: ANGULAR RECONSTITUTION |