EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
ジャーナル・号・ページ	EMBO Rep, Vol. 24, Issue 12, Page e57984, Year 2023
掲載日	2023年12月6日
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 /
PubMed 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.
リンク	EMBO Rep / PubMed:37921038 / PubMed Central
手法	EM (単粒子)
解像度	2.12 - 10.02 Å
構造データ	17879 8ptw EMDB-17879, PDB-8ptw: Chaetomium thermophilum Rix1-complex 手法: EM (単粒子) / 解像度: 2.91 Å EMDB-17880: Chaetomium thermophilum low-resolution Rixosome 手法: EM (単粒子) / 解像度: 10.02 Å EMDB-17881: Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - local refinement - 5S RNP/Rsa4-E117D 手法: EM (単粒子) / 解像度: 2.26 Å EMDB-17882: Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - local refinement - Foot 手法: EM (単粒子) / 解像度: 2.3 Å EMDB-17883: Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - local refinement - H68/H69 手法: EM (単粒子) / 解像度: 2.15 Å EMDB-17884: Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - local refinement - Mrt4/uL11 手法: EM (単粒子) / 解像度: 2.18 Å EMDB-17885: Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - local refinement - UTP30-ITS2 手法: EM (単粒子) / 解像度: 2.38 Å EMDB-17886: Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - consensus refinement 手法: EM (単粒子) / 解像度: 2.12 Å EMDB-17887: Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - local refinement - 5S RNP/Rsa4-E117D 手法: EM (単粒子) / 解像度: 3.02 Å EMDB-17888: Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - local refinement - Foot 手法: EM (単粒子) / 解像度: 3.09 Å EMDB-17889: Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - local refinement - uL1 stalk 手法: EM (単粒子) / 解像度: 3.11 Å EMDB-17890: Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - local refinement - Sda1-Ipi1 手法: EM (単粒子) / 解像度: 4.13 Å EMDB-17891: Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - local refinement - (Rix1)2-(Ipi3)2 手法: EM (単粒子) / 解像度: 3.48 Å EMDB-17892: Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - consensus refinement 手法: EM (単粒子) / 解像度: 2.9 Å EMDB-17893: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - CP 手法: EM (単粒子) / 解像度: 3.55 Å EMDB-17894: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - uL1 stalk 手法: EM (単粒子) / 解像度: 3.13 Å EMDB-17895: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - (Rix1)2-(Ipi3)2 手法: EM (単粒子) / 解像度: 3.4 Å EMDB-17896: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - Foot 手法: EM (単粒子) / 解像度: 3.17 Å EMDB-17897: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - uL1-Nop53N 手法: EM (単粒子) / 解像度: 2.91 Å EMDB-17898: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - consensus refinement 手法: EM (単粒子) / 解像度: 2.94 Å EMDB-17899: Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - local refinement - CP 手法: EM (単粒子) / 解像度: 3.1 Å EMDB-17900: Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - local refinement - uL1 stalk 手法: EM (単粒子) / 解像度: 3.09 Å EMDB-17901: Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - local refinement - (Rix1)2-(Ipi3)2 手法: EM (単粒子) / 解像度: 3.35 Å EMDB-17902: Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - consensus refinement 手法: EM (単粒子) / 解像度: 2.91 Å EMDB-17903: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - 5S RNP/Rsa4-E117D 手法: EM (単粒子) / 解像度: 2.79 Å EMDB-17904: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - uL1-Nop53N 手法: EM (単粒子) / 解像度: 2.56 Å EMDB-17905: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - Foot 手法: EM (単粒子) / 解像度: 2.81 Å EMDB-17906: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - uL1-5S-tip 手法: EM (単粒子) / 解像度: 3.97 Å EMDB-17907: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - consensus refinement 手法: EM (単粒子) / 解像度: 2.55 Å EMDB-17908: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - local refinement - 5S RNP/Rsa4-E117D 手法: EM (単粒子) / 解像度: 2.78 Å EMDB-17909: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - local refinement - Foot 手法: EM (単粒子) / 解像度: 2.82 Å EMDB-17910: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - consensus refinement 手法: EM (単粒子) / 解像度: 2.56 Å EMDB-17911: Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - local refinement - 5S RNP/Rsa4-E117D 手法: EM (単粒子) / 解像度: 2.44 Å EMDB-17912: Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - local refinement - Foot 手法: EM (単粒子) / 解像度: 2.51 Å EMDB-17913: Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - consensus refinement 手法: EM (単粒子) / 解像度: 2.19 Å EMDB-17914: Chaetomium thermophilum pre-60S State 8 - pre-5S rotation without Foot - local refinement - 5S RNP/Rsa4-E117D 手法: EM (単粒子) / 解像度: 3.03 Å EMDB-17915: Chaetomium thermophilum pre-60S State 8 - pre-5S rotation without Foot - consensus refinement 手法: EM (単粒子) / 解像度: 2.86 Å EMDB-17916: Chaetomium thermophilum pre-60S State 9 - pre-5S rotation - immature H68/H69 - local refinement - 5S RNP/Rsa4-E117D 手法: EM (単粒子) / 解像度: 3.02 Å EMDB-17917: Chaetomium thermophilum pre-60S State 9 - pre-5S rotation - immature H68/H69 - local refinement - Foot 手法: EM (単粒子) / 解像度: 3.05 Å EMDB-17918: Chaetomium thermophilum pre-60S State 9 - pre-5S rotation - immature H68/H69 - consensus refinement 手法: EM (単粒子) / 解像度: 2.8 Å EMDB-17919: Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 - local refinement - 5S RNP/Rsa4-E117D 手法: EM (単粒子) / 解像度: 2.88 Å EMDB-17920: Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 - local refinement - Foot 手法: EM (単粒子) / 解像度: 2.89 Å EMDB-17921: Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 - local refinement - Ytm1-Erb1 手法: EM (単粒子) / 解像度: 2.88 Å EMDB-17922: Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 - consensus refinement 手法: EM (単粒子) / 解像度: 2.63 Å EMDB-17923: Chaetomium thermophilum Rix1-complex - (Rix1)2-(Ipi3)2-Ipi1 手法: EM (単粒子) / 解像度: 3.14 Å 17949 8puw EMDB-17949, PDB-8puw: Chaetomium thermophilum Las1-Grc3-complex 手法: EM (単粒子) / 解像度: 3.01 Å 17950 8pv1 EMDB-17950, PDB-8pv1: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - composite structure 手法: EM (単粒子) / 解像度: 2.56 Å 17951 8pv2 EMDB-17951, PDB-8pv2: Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 手法: EM (単粒子) / 解像度: 2.63 Å 17952 8pv3 EMDB-17952, PDB-8pv3: Chaetomium thermophilum pre-60S State 9 - pre-5S rotation - immature H68/H69 - composite structure 手法: EM (単粒子) / 解像度: 2.8 Å 17953 8pv4 EMDB-17953, PDB-8pv4: Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - composite structure 手法: EM (単粒子) / 解像度: 2.9 Å 17954 8pv5 EMDB-17954, PDB-8pv5: Chaetomium thermophilum pre-60S State 8 - pre-5S rotation without Foot - composite structure 手法: EM (単粒子) / 解像度: 2.86 Å 17955 8pv6 EMDB-17955, PDB-8pv6: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - composite structure 手法: EM (単粒子) / 解像度: 2.94 Å 17956 8pv7 EMDB-17956, PDB-8pv7: Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - Composite structure 手法: EM (単粒子) / 解像度: 2.12 Å 17957 8pv8 EMDB-17957, PDB-8pv8: Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - composite structure 手法: EM (単粒子) / 解像度: 2.91 Å 17969 8pvk EMDB-17969, PDB-8pvk: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - composite structure 手法: EM (単粒子) / 解像度: 2.55 Å 17970 8pvl EMDB-17970, PDB-8pvl: Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - composite structure 手法: EM (単粒子) / 解像度: 2.19 Å
化合物	ChemComp-GTP: GUANOSINE-5'-TRIPHOSPHATE / GTP / GTP, エネルギー貯蔵分子YM / グアノシン三リン酸 ChemComp-MG: Unknown entry / マグネシウムジカチオン ChemComp-ZN: Unknown entry ChemComp-HOH*: WATER / 水
由来	thermochaetoides thermophila dsm 1495 (菌類)
キーワード	RIBOSOME (リボソーム) / biogenesis (自然発生説) / pre-60S / 5S RNP