+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-25441 | |||||||||
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タイトル | Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Processome Isolated from R2TP-depleted Yeast Cells | |||||||||
マップデータ | Composite map | |||||||||
試料 |
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キーワード | Bfr2 / Lcp5 / Small subunit processome / RIBOSOMAL PROTEIN / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 rRNA cytidine N-acetyltransferase activity / Noc4p-Nop14p complex / rRNA acetylation involved in maturation of SSU-rRNA / box H/ACA snoRNA binding / tRNA N-acetyltransferase activity / regulation of ribosomal protein gene transcription by RNA polymerase II / t-UTP complex / rRNA small subunit pseudouridine methyltransferase Nep1 / tRNA acetylation / RNA fragment catabolic process ...rRNA cytidine N-acetyltransferase activity / Noc4p-Nop14p complex / rRNA acetylation involved in maturation of SSU-rRNA / box H/ACA snoRNA binding / tRNA N-acetyltransferase activity / regulation of ribosomal protein gene transcription by RNA polymerase II / t-UTP complex / rRNA small subunit pseudouridine methyltransferase Nep1 / tRNA acetylation / RNA fragment catabolic process / CURI complex / UTP-C complex / rRNA 2'-O-methylation / Pwp2p-containing subcomplex of 90S preribosome / histone H2AQ104 methyltransferase activity / endonucleolytic cleavage in ITS1 upstream of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear microtubule / Mpp10 complex / snoRNA guided rRNA 2'-O-methylation / rRNA (pseudouridine) methyltransferase activity / regulation of rRNA processing / endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / box C/D sno(s)RNA binding / septum digestion after cytokinesis / box C/D sno(s)RNA 3'-end processing / regulation of transcription by RNA polymerase I / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rRNA methyltransferase activity / rDNA heterochromatin / single-stranded telomeric DNA binding / box C/D methylation guide snoRNP complex / tRNA export from nucleus / rRNA base methylation / 90S preribosome assembly / rRNA primary transcript binding / sno(s)RNA-containing ribonucleoprotein complex / small nuclear ribonucleoprotein complex / mTORC1-mediated signalling / O-methyltransferase activity / Protein hydroxylation / rRNA methylation / poly(U) RNA binding / U3 snoRNA binding / mRNA modification / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / poly(A)+ mRNA export from nucleus / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / preribosome, small subunit precursor / Ribosomal scanning and start codon recognition / snoRNA binding / establishment of cell polarity / positive regulation of transcription by RNA polymerase I / Major pathway of rRNA processing in the nucleolus and cytosol / nucleolar large rRNA transcription by RNA polymerase I / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / proteasome assembly / 90S preribosome / regulation of translational fidelity / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / RNA processing / 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) / vesicle-mediated transport / enzyme activator activity / 転移酵素; アシル基を移すもの; アミノアシル基以外のアシル基を移すもの / RNA endonuclease activity / ribosome assembly / nuclear periphery / 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / translational initiation / maintenance of translational fidelity / rRNA processing / ribosomal small subunit biogenesis / unfolded protein binding / small ribosomal subunit rRNA binding / protein transport / ribosome biogenesis / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / nucleolus / mitochondrion / RNA binding 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (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: 3.99 Å | |||||||||
データ登録者 | Rai J / Zhao Y / Li H | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Commun Biol / 年: 2022 タイトル: Artificial intelligence-assisted cryoEM structure of Bfr2-Lcp5 complex observed in the yeast small subunit processome. 著者: Yu Zhao / Jay Rai / Chong Xu / Huan He / Hong Li / 要旨: Eukaryotic ribosome is maturated through an elaborate process that includes modification, processing and folding of pre-ribosomal RNA (pre-rRNAs) by a series of ribosome assembly intermediates. More ...Eukaryotic ribosome is maturated through an elaborate process that includes modification, processing and folding of pre-ribosomal RNA (pre-rRNAs) by a series of ribosome assembly intermediates. More than 70 factors participate in the dynamic assembly and disassembly of the small subunit processome (90S) inside nucleolus, leading to the early maturation of small subunit. The 5' domain of the 18S rRNA is the last to be incorporated into the stable 90S prior to the cleavage of pre-rRNA at the A1 site. This step is facilitated by the Kre33-Enp2-Bfr2-Lcp5 protein module with the participation of the DEAD-box protein Dbp4. Though structures of Kre33 and Enp2 have been modeled in previously observed 90S structures, that of Bfr2-Lcp5 complex remains unavailable. Here, we report an AlphaFold-assisted structure determination of the Bfr2-Lcp5 complex captured in a 3.99 Å - 7.24 Å cryoEM structure of 90S isolated from yeast cells depleted of Pih1, a chaperone protein of the 90S core assembly. The structure model is consistent with the protein-protein interaction results and the secondary structures of recombinant Bfr2 and Bfr2-Lcp5 complex obtained by Circular Dichroism. The Bfr2-Lcp5 complex interaction mimics that of exosome factors Rrp6-Rrp47 and acts to regulate 90S transitions. | |||||||||
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_25441.map.gz | 279.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-25441-v30.xml emd-25441.xml | 100.6 KB 100.6 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_25441.png | 99.5 KB | ||
その他 | emd_25441_additional_1.map.gz emd_25441_additional_2.map.gz emd_25441_additional_3.map.gz | 288.4 MB 286.7 MB 282.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-25441 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25441 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_25441_validation.pdf.gz | 631.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_25441_full_validation.pdf.gz | 630.7 KB | 表示 | |
XML形式データ | emd_25441_validation.xml.gz | 7.3 KB | 表示 | |
CIF形式データ | emd_25441_validation.cif.gz | 8.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25441 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25441 | HTTPS FTP |
-関連構造データ
関連構造データ | 7sukMC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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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_25441.map.gz / 形式: CCP4 / 大きさ: 307.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Composite 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: 1.074 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
-追加マップ: Core region (3.99 Angstorm) from 199,534 particles.
ファイル | emd_25441_additional_1.map | ||||||||||||
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注釈 | Core region (3.99 Angstorm) from 199,534 particles. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Central Domain (7.24 Angstorm) from 199,534 particles.
ファイル | emd_25441_additional_2.map | ||||||||||||
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注釈 | Central Domain (7.24 Angstorm) from 199,534 particles. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Head domain (5.04 Angstorm) from 84,570 particles.
ファイル | emd_25441_additional_3.map | ||||||||||||
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注釈 | Head domain (5.04 Angstorm) from 84,570 particles. | ||||||||||||
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 : Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Proc...
+超分子 #1: Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Proc...
+分子 #1: U3 small nucleolar RNA-associated protein MPP10
+分子 #2: Nucleolar protein 56
+分子 #3: Something about silencing protein 10
+分子 #6: 40S ribosomal protein S18-A
+分子 #7: 40S ribosomal protein S4-A
+分子 #8: 40S ribosomal protein S5
+分子 #9: 40S ribosomal protein S7-A
+分子 #10: 40S ribosomal protein S8-A
+分子 #11: 40S ribosomal protein S9-A
+分子 #12: 40S ribosomal protein S16-A
+分子 #13: 40S ribosomal protein S11-A
+分子 #14: 40S ribosomal protein S22-A
+分子 #15: 40S ribosomal protein S24-A
+分子 #16: 40S ribosomal protein S28-A
+分子 #17: NET1-associated nuclear protein 1
+分子 #18: U3 small nucleolar RNA-associated protein 15
+分子 #19: U3 small nucleolar RNA-associated protein 9
+分子 #20: U3 small nucleolar RNA-associated protein 5
+分子 #21: U3 small nucleolar RNA-associated protein 10
+分子 #22: U3 small nucleolar RNA-associated protein 4
+分子 #23: Periodic tryptophan protein 2
+分子 #24: U3 small nucleolar RNA-associated protein 6
+分子 #25: U3 small nucleolar RNA-associated protein 12
+分子 #26: U3 small nucleolar RNA-associated protein 18
+分子 #27: U3 small nucleolar RNA-associated protein 21
+分子 #28: Protein SOF1
+分子 #29: Ribosome biogenesis protein ENP2
+分子 #30: U3 small nucleolar RNA-associated protein 7
+分子 #31: U3 small nucleolar ribonucleoprotein protein IMP3
+分子 #32: 40S ribosomal protein S14-B
+分子 #33: KRR1 small subunit processome component
+分子 #34: rRNA 2'-O-methyltransferase fibrillarin
+分子 #35: Ribonucloprotein
+分子 #36: RRP9 isoform 1
+分子 #37: RNA 3'-terminal phosphate cyclase-like protein
+分子 #38: Ribosome biogenesis protein BMS1
+分子 #39: Ribosomal RNA small subunit methyltransferase NEP1
+分子 #40: rRNA-processing protein FCF1
+分子 #41: U3 small nucleolar ribonucleoprotein protein IMP4
+分子 #42: Ribosome biogenesis protein UTP30
+分子 #43: Pre-rRNA-processing protein PNO1
+分子 #44: rRNA-processing protein FCF2
+分子 #45: 40S ribosomal protein S23-A
+分子 #46: U3 small nucleolar RNA-associated protein 14
+分子 #47: Nucleolar complex protein 14
+分子 #48: U3 small nucleolar RNA-associated protein 11
+分子 #49: Essential nuclear protein 1
+分子 #50: rRNA biogenesis protein RRP5
+分子 #51: U3 small nucleolar RNA-associated protein 22
+分子 #52: Ribosomal RNA-processing protein 7
+分子 #54: Nucleolar complex protein 4
+分子 #55: U3 small nucleolar RNA-associated protein 8
+分子 #56: Bud site selection protein 21
+分子 #57: U3 small nucleolar RNA-associated protein 13
+分子 #58: Protein FAF1
+分子 #59: Nucleolar protein 58
+分子 #60: Regulator of rDNA transcription protein 14
+分子 #61: U3 small nucleolar RNA-associated protein 20
+分子 #62: RNA cytidine acetyltransferase
+分子 #63: 40S ribosomal protein S6-A
+分子 #64: 40S ribosomal protein S13
+分子 #65: Protein BFR2
+分子 #66: U3 small nucleolar ribonucleoprotein protein LCP5
+分子 #4: 5' ETS
+分子 #5: U3 snoRNA
+分子 #53: 18S pre-rRNA
-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: 7.7 |
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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 K3 BIOQUANTUM (6k x 4k) 平均電子線量: 1.074 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 / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 1.3 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: NONE |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.99 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 199534 |
初期 角度割当 | タイプ: NOT APPLICABLE |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |