+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4636 | |||||||||
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タイトル | Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | 60S subunit / eIF6 / Nmd3 / Lsg1 / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 mating projection tip / 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) / response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit binding ...mating projection tip / 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) / response to cycloheximide / 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 / preribosome, large subunit precursor / 加水分解酵素; 酸無水物に作用; リン含有酸無水物に作用 / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / regulation of translational fidelity / protein-RNA complex assembly / ribosomal subunit export from nucleus / translational termination / 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 / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / translational initiation / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / protein transport / ribosome biogenesis / viral capsid / ribosomal large subunit assembly / protein-macromolecule adaptor activity / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / response to antibiotic / GTPase activity / mRNA binding / ubiquitin protein ligase 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 (パン酵母) / Saccharomyces cerevisiae | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.5 Å | |||||||||
データ登録者 | Kargas V / Warren AJ | |||||||||
資金援助 | 英国, 2件
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引用 | ジャーナル: Elife / 年: 2019 タイトル: Mechanism of completion of peptidyltransferase centre assembly in eukaryotes. 著者: Vasileios Kargas / Pablo Castro-Hartmann / Norberto Escudero-Urquijo / Kyle Dent / Christine Hilcenko / Carolin Sailer / Gertrude Zisser / Maria J Marques-Carvalho / Simone Pellegrino / ...著者: Vasileios Kargas / Pablo Castro-Hartmann / Norberto Escudero-Urquijo / Kyle Dent / Christine Hilcenko / Carolin Sailer / Gertrude Zisser / Maria J Marques-Carvalho / Simone Pellegrino / Leszek Wawiórka / Stefan Mv Freund / Jane L Wagstaff / Antonina Andreeva / Alexandre Faille / Edwin Chen / Florian Stengel / Helmut Bergler / Alan John Warren / 要旨: During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase ...During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase centre (PTC) completion that explains how integration of the last ribosomal proteins is coupled to release of the nuclear export adaptor Nmd3. Single-particle cryo-EM reveals that eL40 recruitment stabilises helix 89 to form the uL16 binding site. The loading of uL16 unhooks helix 38 from Nmd3 to adopt its mature conformation. In turn, partial retraction of the L1 stalk is coupled to a conformational switch in Nmd3 that allows the uL16 P-site loop to fully accommodate into the PTC where it competes with Nmd3 for an overlapping binding site (base A2971). Our data reveal how the central functional site of the ribosome is sculpted and suggest how the formation of translation-competent 60S subunits is disrupted in leukaemia-associated ribosomopathies. | |||||||||
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_4636.map.gz | 20.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4636-v30.xml emd-4636.xml | 64.8 KB 64.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_4636.png | 70 KB | ||
Filedesc metadata | emd-4636.cif.gz | 14.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4636 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4636 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_4636_validation.pdf.gz | 261.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_4636_full_validation.pdf.gz | 260.3 KB | 表示 | |
XML形式データ | emd_4636_validation.xml.gz | 6.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4636 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4636 | 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_4636.map.gz / 形式: CCP4 / 大きさ: 178 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: 1.065 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 : Lsg1-TAP 60s ribosomal subunit
+超分子 #1: Lsg1-TAP 60s ribosomal subunit
+分子 #1: 25S rRNA
+分子 #47: 5S rRNA
+分子 #48: 5.8S rRNA
+分子 #2: 60S ribosomal protein L2-A
+分子 #3: 60S ribosomal protein L3
+分子 #4: 60S ribosomal protein L4-A
+分子 #5: 60S ribosomal protein L11-A
+分子 #6: 60S ribosomal protein L9-A
+分子 #7: 60S ribosomal protein L6-A
+分子 #8: 60S ribosomal protein L8-A
+分子 #9: 60S ribosomal protein L16-B
+分子 #10: 60S ribosomal protein L13-A
+分子 #11: 60S ribosomal protein L23-A
+分子 #12: 60S ribosomal protein L14-A
+分子 #13: 60S ribosomal protein L28
+分子 #14: 60S ribosomal protein L15-A
+分子 #15: 60S ribosomal protein L5
+分子 #16: 60S ribosomal protein L18-A
+分子 #17: 60S ribosomal protein L19-A
+分子 #18: 60S ribosomal protein L20-A
+分子 #19: 60S ribosomal protein L21-A
+分子 #20: 60S ribosomal protein L17-A
+分子 #21: 60S ribosomal protein L22-A
+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 L35-A
+分子 #26: 60S ribosomal protein L29
+分子 #27: 60S ribosomal protein L7-A
+分子 #28: 60S ribosomal protein L30
+分子 #29: 60S ribosomal protein L31-A
+分子 #30: 60S ribosomal protein L32
+分子 #31: 60S ribosomal protein L33-A
+分子 #32: 60S ribosomal protein L34-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: 60S ribosomal protein L39
+分子 #37: 60S ribosomal protein L42-A
+分子 #38: 60S ribosomal protein L43-A
+分子 #39: Eukaryotic translation initiation factor 6
+分子 #40: Cytoplasmic 60S subunit biogenesis factor REH1
+分子 #41: 60S ribosomal export protein NMD3
+分子 #42: 60S ribosomal protein L24-A
+分子 #43: Large subunit GTPase 1
+分子 #44: uL1
+分子 #45: 60S ribosomal protein L10
+分子 #46: Ubiquitin-60S ribosomal protein L40
+分子 #49: 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 III (4k x 4k) 平均電子線量: 63.0 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: FLOOD BEAM / 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
初期モデル | モデルのタイプ: OTHER |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / 解像度のタイプ: BY AUTHOR / 解像度: 3.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 2.1) / 使用した粒子像数: 48239 |
初期 角度割当 | タイプ: ANGULAR RECONSTITUTION / ソフトウェア - 名称: RELION |
最終 角度割当 | タイプ: ANGULAR RECONSTITUTION |