+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-17955 | |||||||||
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タイトル | Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - composite structure | |||||||||
マップデータ | Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - composite structure | |||||||||
試料 |
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キーワード | biogenesis / pre-60S / 5S RNP / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 rixosome complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / PeBoW complex / nuclear pre-replicative complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein kinase regulator activity / maturation of 5.8S rRNA / ribosomal large subunit binding ...rixosome complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / protein N-linked glycosylation via asparagine / PeBoW complex / nuclear pre-replicative complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein kinase regulator activity / maturation of 5.8S rRNA / ribosomal large subunit binding / nuclear-transcribed mRNA catabolic process / preribosome, large subunit precursor / MLL1 complex / ribosomal large subunit export from nucleus / protein-RNA complex assembly / post-translational protein modification / ribosomal subunit export from nucleus / ribonucleoprotein complex binding / translation initiation factor activity / maturation of LSU-rRNA / cellular response to amino acid starvation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / assembly of large subunit precursor of preribosome / cytosolic ribosome assembly / ribosomal large subunit biogenesis / DNA-templated DNA replication / rRNA processing / protein transport / ribosome biogenesis / regulation of translation / 5S rRNA binding / large ribosomal subunit rRNA binding / nucleic acid binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / nucleolus / GTP binding / RNA binding / zinc ion binding / nucleoplasm / membrane / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Thermochaetoides thermophila DSM 1495 (菌類) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.94 Å | |||||||||
データ登録者 | Thoms M / Cheng J / Denk T / Berninghausen O / Beckmann R | |||||||||
資金援助 | European Union, 1件
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引用 | ジャーナル: EMBO Rep / 年: 2023 タイトル: Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation. 著者: Matthias Thoms / Benjamin Lau / Jingdong Cheng / Lisa Fromm / Timo Denk / Nikola Kellner / Dirk Flemming / Paulina Fischer / Laurent Falquet / Otto Berninghausen / Roland Beckmann / Ed Hurt / 要旨: The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. Here, we isolate and describe the conserved rixosome from ...The rixosome defined in Schizosaccharomyces pombe and humans performs diverse roles in pre-ribosomal RNA processing and gene silencing. Here, we isolate and describe the conserved rixosome from Chaetomium thermophilum, which consists of two sub-modules, the sphere-like Rix1-Ipi3-Ipi1 and the butterfly-like Las1-Grc3 complex, connected by a flexible linker. The Rix1 complex of the rixosome utilizes Sda1 as landing platform on nucleoplasmic pre-60S particles to wedge between the 5S rRNA tip and L1-stalk, thereby facilitating the 180° rotation of the immature 5S RNP towards its mature conformation. Upon rixosome positioning, the other sub-module with Las1 endonuclease and Grc3 polynucleotide-kinase can reach a strategic position at the pre-60S foot to cleave and 5' phosphorylate the nearby ITS2 pre-rRNA. Finally, inward movement of the L1 stalk permits the flexible Nop53 N-terminus with its AIM motif to become positioned at the base of the L1-stalk to facilitate Mtr4 helicase-exosome participation for completing ITS2 removal. Thus, the rixosome structure elucidates the coordination of two central ribosome biogenesis events, but its role in gene silencing may adapt similar strategies. | |||||||||
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_17955.map.gz | 20.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-17955-v30.xml emd-17955.xml | 94.7 KB 94.7 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_17955.png | 122.2 KB | ||
Filedesc metadata | emd-17955.cif.gz | 22 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-17955 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-17955 | HTTPS FTP |
-関連構造データ
関連構造データ | 8pv6MC 8ptwC 8puwC 8pv1C 8pv2C 8pv3C 8pv4C 8pv5C 8pv7C 8pv8C 8pvkC 8pvlC 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_17955.map.gz / 形式: CCP4 / 大きさ: 476.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - composite structure | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.045 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
-試料の構成要素
+全体 : Chaetomium thermophilum pre-60S State 3 - post-5S rotation with R...
+超分子 #1: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with R...
+超分子 #2: Ribosome
+超分子 #3: Ribosome assembly protein 4
+分子 #1: 26S rRNA
+分子 #2: 5.8S rRNA
+分子 #3: ITS2
+分子 #4: 5S rRNA
+分子 #5: Large ribosomal subunit protein uL10
+分子 #6: Nucleolar GTP-binding protein 1
+分子 #7: Putative RNA-binding protein
+分子 #8: Pescadillo homolog
+分子 #9: Ribosome biogenesis protein NSA2 homolog
+分子 #10: Putative GTP binding protein
+分子 #11: 60S ribosomal protein l7-like protein
+分子 #12: Eukaryotic translation initiation factor 6
+分子 #13: DUF2423 domain-containing protein
+分子 #14: Ribosome biogenesis protein RLP24
+分子 #15: Protein SDA1
+分子 #16: Pre-rRNA-processing protein IPI1
+分子 #17: Pre-rRNA-processing protein IPI3
+分子 #18: Pre-rRNA-processing protein RIX1
+分子 #19: Zinc finger domain-containing protein
+分子 #20: Nucleolar GTP-binding protein 2
+分子 #21: Ribosome biogenesis protein NOP53
+分子 #22: Ribosome assembly protein 4
+分子 #23: rRNA-processing protein
+分子 #24: 60S ribosomal protein L2-like protein
+分子 #25: 60S ribosomal protein L3-like protein
+分子 #26: 60S ribosomal protein L4-like protein
+分子 #27: 60S ribosomal protein l5-like protein
+分子 #28: 60S ribosomal protein L6
+分子 #29: 60S ribosomal protein L8
+分子 #30: 60S ribosomal protein l9-like protein
+分子 #31: Putative ribosomal protein
+分子 #32: 60S ribosomal protein L12-like protein
+分子 #33: 60S ribosomal protein L13
+分子 #34: 60S ribosomal protein L14-like protein
+分子 #35: Ribosomal protein L15
+分子 #36: 60S ribosomal protein L16-like protein
+分子 #37: 60S ribosomal protein l17-like protein
+分子 #38: Ribosomal protein L18-like protein
+分子 #39: Ribosomal protein L19
+分子 #40: 60S ribosomal protein L20
+分子 #41: 60S ribosomal protein l21-like protein
+分子 #42: 60S ribosomal protein L22-like protein
+分子 #43: 60S ribosomal protein l23-like protein
+分子 #44: 60S ribosomal protein L25-like protein
+分子 #45: 60S ribosomal protein L26-like protein
+分子 #46: 60S ribosomal protein L27
+分子 #47: 60S ribosomal protein L28-like protein
+分子 #48: 60S ribosomal protein L29
+分子 #49: 60S ribosomal protein l30-like protein
+分子 #50: Putative 60S ribosomal protein
+分子 #51: 60S ribosomal protein L32-like protein
+分子 #52: 60S ribosomal protein l33-like protein
+分子 #53: Ribosomal protein l34-like protein
+分子 #54: dolichyl-diphosphooligosaccharide--protein glycotransferase
+分子 #55: 60S ribosomal protein L36
+分子 #56: Ribosomal protein L37
+分子 #57: 60S ribosomal protein L38-like protein
+分子 #58: Ribosomal protein eL39
+分子 #59: 60S ribosomal protein L43-like protein
+分子 #60: Putative 60S ribosomal protein
+分子 #61: Ribosomal protein
+分子 #62: GUANOSINE-5'-TRIPHOSPHATE
+分子 #63: MAGNESIUM ION
+分子 #64: ZINC ION
+分子 #65: water
-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) 検出モード: COUNTING / 平均電子線量: 46.0 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: SPOT SCAN / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3.5 µm / 最小 デフォーカス(公称値): 0.4 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: 2.94 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 25753 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |