Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Journal, issue, pages	EMBO Rep, Vol. 24, Issue 12, Page e57984, Year 2023
Publish date	Dec 6, 2023
Authors	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 Abstract	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.
External links	EMBO Rep / PubMed:37921038 / PubMed Central
Methods	EM (single particle)
Resolution	2.12 - 10.02 Å
Structure data	17879 8ptw EMDB-17879, PDB-8ptw: Chaetomium thermophilum Rix1-complex Method: EM (single particle) / Resolution: 2.91 Å EMDB-17880: Chaetomium thermophilum low-resolution Rixosome Method: EM (single particle) / Resolution: 10.02 Å EMDB-17881: Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - local refinement - 5S RNP/Rsa4-E117D Method: EM (single particle) / Resolution: 2.26 Å EMDB-17882: Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - local refinement - Foot Method: EM (single particle) / Resolution: 2.3 Å EMDB-17883: Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - local refinement - H68/H69 Method: EM (single particle) / Resolution: 2.15 Å EMDB-17884: Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - local refinement - Mrt4/uL11 Method: EM (single particle) / Resolution: 2.18 Å EMDB-17885: Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - local refinement - UTP30-ITS2 Method: EM (single particle) / Resolution: 2.38 Å EMDB-17886: Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - consensus refinement Method: EM (single particle) / Resolution: 2.12 Å EMDB-17887: Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - local refinement - 5S RNP/Rsa4-E117D Method: EM (single particle) / Resolution: 3.02 Å EMDB-17888: Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - local refinement - Foot Method: EM (single particle) / Resolution: 3.09 Å EMDB-17889: Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - local refinement - uL1 stalk Method: EM (single particle) / Resolution: 3.11 Å EMDB-17890: Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - local refinement - Sda1-Ipi1 Method: EM (single particle) / Resolution: 4.13 Å EMDB-17891: Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - local refinement - (Rix1)2-(Ipi3)2 Method: EM (single particle) / Resolution: 3.48 Å EMDB-17892: Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - consensus refinement Method: EM (single particle) / Resolution: 2.9 Å EMDB-17893: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - CP Method: EM (single particle) / Resolution: 3.55 Å EMDB-17894: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - uL1 stalk Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 3.4 Å EMDB-17896: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - Foot Method: EM (single particle) / Resolution: 3.17 Å EMDB-17897: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - local refinement - uL1-Nop53N Method: EM (single particle) / Resolution: 2.91 Å EMDB-17898: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - consensus refinement Method: EM (single particle) / Resolution: 2.94 Å EMDB-17899: Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - local refinement - CP Method: EM (single particle) / Resolution: 3.1 Å EMDB-17900: Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - local refinement - uL1 stalk Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 3.35 Å EMDB-17902: Chaetomium thermophilum pre-60S State 4 - post-5S rotation with Rix1 complex without Foot - consensus refinement Method: EM (single particle) / Resolution: 2.91 Å EMDB-17903: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - 5S RNP/Rsa4-E117D Method: EM (single particle) / Resolution: 2.79 Å EMDB-17904: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - uL1-Nop53N Method: EM (single particle) / Resolution: 2.56 Å EMDB-17905: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - Foot Method: EM (single particle) / Resolution: 2.81 Å EMDB-17906: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - local refinement - uL1-5S-tip Method: EM (single particle) / Resolution: 3.97 Å EMDB-17907: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - consensus refinement Method: EM (single particle) / Resolution: 2.55 Å EMDB-17908: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - local refinement - 5S RNP/Rsa4-E117D Method: EM (single particle) / Resolution: 2.78 Å EMDB-17909: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - local refinement - Foot Method: EM (single particle) / Resolution: 2.82 Å EMDB-17910: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - consensus refinement Method: EM (single particle) / Resolution: 2.56 Å EMDB-17911: Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - local refinement - 5S RNP/Rsa4-E117D Method: EM (single particle) / Resolution: 2.44 Å EMDB-17912: Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - local refinement - Foot Method: EM (single particle) / Resolution: 2.51 Å EMDB-17913: Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - consensus refinement Method: EM (single particle) / Resolution: 2.19 Å EMDB-17914: Chaetomium thermophilum pre-60S State 8 - pre-5S rotation without Foot - local refinement - 5S RNP/Rsa4-E117D Method: EM (single particle) / Resolution: 3.03 Å EMDB-17915: Chaetomium thermophilum pre-60S State 8 - pre-5S rotation without Foot - consensus refinement Method: EM (single particle) / Resolution: 2.86 Å EMDB-17916: Chaetomium thermophilum pre-60S State 9 - pre-5S rotation - immature H68/H69 - local refinement - 5S RNP/Rsa4-E117D Method: EM (single particle) / Resolution: 3.02 Å EMDB-17917: Chaetomium thermophilum pre-60S State 9 - pre-5S rotation - immature H68/H69 - local refinement - Foot Method: EM (single particle) / Resolution: 3.05 Å EMDB-17918: Chaetomium thermophilum pre-60S State 9 - pre-5S rotation - immature H68/H69 - consensus refinement Method: EM (single particle) / Resolution: 2.8 Å EMDB-17919: Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 - local refinement - 5S RNP/Rsa4-E117D Method: EM (single particle) / Resolution: 2.88 Å EMDB-17920: Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 - local refinement - Foot Method: EM (single particle) / Resolution: 2.89 Å EMDB-17921: Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 - local refinement - Ytm1-Erb1 Method: EM (single particle) / Resolution: 2.88 Å EMDB-17922: Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 - consensus refinement Method: EM (single particle) / Resolution: 2.63 Å EMDB-17923: Chaetomium thermophilum Rix1-complex - (Rix1)2-(Ipi3)2-Ipi1 Method: EM (single particle) / Resolution: 3.14 Å 17949 8puw EMDB-17949, PDB-8puw: Chaetomium thermophilum Las1-Grc3-complex Method: EM (single particle) / Resolution: 3.01 Å 17950 8pv1 EMDB-17950, PDB-8pv1: Chaetomium thermophilum pre-60S State 6 - pre-5S rotation - L1 intermediate - composite structure Method: EM (single particle) / Resolution: 2.56 Å 17951 8pv2 EMDB-17951, PDB-8pv2: Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1 Method: EM (single particle) / Resolution: 2.63 Å 17952 8pv3 EMDB-17952, PDB-8pv3: Chaetomium thermophilum pre-60S State 9 - pre-5S rotation - immature H68/H69 - composite structure Method: EM (single particle) / Resolution: 2.8 Å 17953 8pv4 EMDB-17953, PDB-8pv4: Chaetomium thermophilum pre-60S State 2 - pre-5S rotation with Rix1 complex - composite structure Method: EM (single particle) / Resolution: 2.9 Å 17954 8pv5 EMDB-17954, PDB-8pv5: Chaetomium thermophilum pre-60S State 8 - pre-5S rotation without Foot - composite structure Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 2.94 Å 17956 8pv7 EMDB-17956, PDB-8pv7: Chaetomium thermophilum pre-60S State 1 - pre-5S rotation (Arx1/Nog2 state) - Composite structure Method: EM (single particle) / Resolution: 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 Method: EM (single particle) / Resolution: 2.91 Å 17969 8pvk EMDB-17969, PDB-8pvk: Chaetomium thermophilum pre-60S State 5 - pre-5S rotation - L1 inward - composite structure Method: EM (single particle) / Resolution: 2.55 Å 17970 8pvl EMDB-17970, PDB-8pvl: Chaetomium thermophilum pre-60S State 7 - pre-5S rotation lacking Utp30/ITS2 - composite structure Method: EM (single particle) / Resolution: 2.19 Å
Chemicals	ChemComp-GTP: GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying moleculeYM / Guanosine triphosphate ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry ChemComp-HOH*: WATER / Water
Source	thermochaetoides thermophila dsm 1495 (fungus)
Keywords	RIBOSOME / biogenesis / pre-60S / 5S RNP