+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-24296 | ||||||||||||
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タイトル | State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model | ||||||||||||
マップデータ | State E1 Overall map | ||||||||||||
試料 |
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キーワード | ribosome biogenesis / DEAD-box ATPases / methyltransferase / nucleolus / RIBOSOME | ||||||||||||
機能・相同性 | 機能・相同性情報 25S rRNA (cytosine2870-C5)-methyltransferase / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc1p-Noc2p complex / snoRNA release from pre-rRNA / Noc2p-Noc3p complex / nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA (uridine-2'-O-)-methyltransferase activity ...25S rRNA (cytosine2870-C5)-methyltransferase / 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase / rRNA (guanosine-2'-O-)-methyltransferase activity / Noc1p-Noc2p complex / snoRNA release from pre-rRNA / Noc2p-Noc3p complex / nuclear division / exonucleolytic trimming to generate mature 5'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / intracellular mRNA localization / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / PeBoW complex / nuclear pre-replicative complex / rRNA base methylation / rRNA primary transcript binding / ATP-dependent activity, acting on RNA / positive regulation of ATP-dependent activity / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methylation / protein folding chaperone complex / 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) / proteasome binding / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / nuclear-transcribed mRNA catabolic process / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / mRNA transport / DNA replication initiation / 90S preribosome / regulation of translational fidelity / protein-RNA complex assembly / ribosomal subunit export from nucleus / ribonucleoprotein complex binding / 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) / translation initiation factor activity / maturation of LSU-rRNA / proteasome complex / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear periphery / assembly of large subunit precursor of preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / cytosolic ribosome assembly / maturation of SSU-rRNA / small-subunit processome / macroautophagy / maintenance of translational fidelity / protein catabolic process / rRNA processing / ribosomal small subunit biogenesis / protein transport / ribosome biogenesis / ribosomal large subunit assembly / nuclear envelope / protein-macromolecule adaptor activity / ATPase binding / large ribosomal subunit rRNA binding / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / RNA helicase activity / negative regulation of translation / rRNA binding / ribosome / RNA helicase / structural constituent of ribosome / translation / cell division / GTPase activity / mRNA binding / chromatin binding / GTP binding / nucleolus / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol 類似検索 - 分子機能 | ||||||||||||
生物種 | Saccharomyces cerevisiae BY4741 (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: 3.04 Å | ||||||||||||
データ登録者 | Cruz VE / Sekulski K / Peddada N / Erzberger JP | ||||||||||||
資金援助 | 米国, 3件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2022 タイトル: Sequence-specific remodeling of a topologically complex RNP substrate by Spb4. 著者: Victor Emmanuel Cruz / Kamil Sekulski / Nagesh Peddada / Carolin Sailer / Sahana Balasubramanian / Christine S Weirich / Florian Stengel / Jan P Erzberger / 要旨: DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular ...DEAD-box ATPases are ubiquitous enzymes essential in all aspects of RNA biology. However, the limited in vitro catalytic activities described for these enzymes are at odds with their complex cellular roles, most notably in driving large-scale RNA remodeling steps during the assembly of ribonucleoproteins (RNPs). We describe cryo-EM structures of 60S ribosomal biogenesis intermediates that reveal how context-specific RNA unwinding by the DEAD-box ATPase Spb4 results in extensive, sequence-specific remodeling of rRNA secondary structure. Multiple cis and trans interactions stabilize Spb4 in a post-catalytic, high-energy intermediate that drives the organization of the three-way junction at the base of rRNA domain IV. This mechanism explains how limited strand separation by DEAD-box ATPases is leveraged to provide non-equilibrium directionality and ensure efficient and accurate RNP assembly. | ||||||||||||
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_24296.map.gz | 249.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-24296-v30.xml emd-24296.xml | 88.8 KB 88.8 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_24296_fsc.xml | 14.9 KB | 表示 | FSCデータファイル |
画像 | emd_24296.png | 169.5 KB | ||
Filedesc metadata | emd-24296.cif.gz | 20 KB | ||
その他 | emd_24296_half_map_1.map.gz emd_24296_half_map_2.map.gz | 239.6 MB 239.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-24296 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24296 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_24296_validation.pdf.gz | 1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_24296_full_validation.pdf.gz | 1 MB | 表示 | |
XML形式データ | emd_24296_validation.xml.gz | 22.5 KB | 表示 | |
CIF形式データ | emd_24296_validation.cif.gz | 29.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24296 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24296 | HTTPS FTP |
-関連構造データ
関連構造データ | 7r7aMC 7nacC 7nadC 7nafC 7r6kC 7r6qC 7r72C 7r7cC 7u0hC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_24296.map.gz / 形式: CCP4 / 大きさ: 282.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | State E1 Overall map | ||||||||||||||||||||||||||||||||||||
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: 1.08 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: State E1 Overall half map 2
ファイル | emd_24296_half_map_1.map | ||||||||||||
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注釈 | State E1 Overall half map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: State E1 Overall half map 1
ファイル | emd_24296_half_map_2.map | ||||||||||||
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注釈 | State E1 Overall half map 1 | ||||||||||||
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 : Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.
+超分子 #1: Nucleolar 60S intermediate purified with tags on Ytm1 and Spb4.
+分子 #1: 25S rRNA
+分子 #2: 5.8S rRNA
+分子 #52: 5.8S ribosomal RNA gene and internal transcribed spacer 2
+分子 #3: 60S ribosomal subunit assembly/export protein LOC1
+分子 #4: Ribosome biogenesis protein BRX1
+分子 #5: 60S ribosomal protein L3
+分子 #6: 60S ribosomal protein L4-A
+分子 #7: 60S ribosomal protein L6-A
+分子 #8: 60S ribosomal protein L7-A
+分子 #9: 60S ribosomal protein L9-A
+分子 #10: rRNA-processing protein EBP2
+分子 #11: 60S ribosomal protein L13-A
+分子 #12: 60S ribosomal protein L14-A
+分子 #13: 60S ribosomal protein L15-A
+分子 #14: 60S ribosomal protein L16-A
+分子 #15: 60S ribosomal protein L17-A
+分子 #16: 60S ribosomal protein L18-A
+分子 #17: 60S ribosomal protein L20-A
+分子 #18: 60S ribosomal protein L21-A
+分子 #19: Ribosome assembly factor MRT4
+分子 #20: 60S ribosomal protein L25
+分子 #21: 60S ribosomal protein L26-A
+分子 #22: Nucleolar GTP-binding protein 1
+分子 #23: 60S ribosomal protein L31-A
+分子 #24: 60S ribosomal protein L32
+分子 #25: 60S ribosomal protein L33-A
+分子 #26: 60S ribosomal protein L35-A
+分子 #27: 60S ribosomal protein L36-A
+分子 #28: 60S ribosomal protein L37-A
+分子 #29: 60S ribosome subunit biogenesis protein NIP7
+分子 #30: Ribosome biogenesis protein ERB1
+分子 #31: 25S rRNA (cytosine(2870)-C(5))-methyltransferase
+分子 #32: Ribosome biogenesis protein NSA2
+分子 #33: Nuclear GTP-binding protein NUG1
+分子 #34: Ribosome biogenesis protein RLP24
+分子 #35: Nucleolar protein 16
+分子 #36: Eukaryotic translation initiation factor 6
+分子 #37: UPF0642 protein YBL028C
+分子 #38: Nucleolar complex protein 2
+分子 #39: Nucleolar complex-associated protein 3
+分子 #40: Proteasome-interacting protein CIC1
+分子 #41: 60S ribosomal protein L23-A
+分子 #42: 60S ribosomal protein L19-A
+分子 #43: 60S ribosomal protein L8-A
+分子 #44: 60S ribosomal protein L27-A
+分子 #45: 60S ribosomal protein L22-A
+分子 #46: 60S ribosomal protein L30
+分子 #47: 60S ribosomal protein L34-A
+分子 #48: 60S ribosomal protein L38
+分子 #49: Pescadillo homolog
+分子 #50: YTM1 isoform 1
+分子 #51: Ribosome biogenesis protein RLP7
+分子 #53: ATP-dependent RNA helicase HAS1
+分子 #54: Ribosome biogenesis protein 15
+分子 #55: 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase
+分子 #56: Ribosomal protein
+分子 #57: ATP-dependent rRNA helicase SPB4
+分子 #58: 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
濃度 | 0.45 mg/mL | ||||||||||||||||||
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緩衝液 | pH: 8 構成要素:
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グリッド | モデル: Quantifoil R2/2 / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 0.3 / 前処理 - タイプ: GLOW DISCHARGE | ||||||||||||||||||
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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撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 1 / 実像数: 4523 / 平均露光時間: 0.05 sec. / 平均電子線量: 1.2 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 70.0 µm / 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): 0.9 µm / 最小 デフォーカス(公称値): 0.2 µm / 倍率(公称値): 81000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | プロトコル: RIGID BODY FIT |
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得られたモデル | PDB-7r7a: |