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Structure paper

TitleStructural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation.
Journal, issue, pagesEMBO Rep, Vol. 24, Issue 12, Page e57984, Year 2023
Publish dateDec 6, 2023
AuthorsMatthias Thoms / Benjamin Lau / Jingdong Cheng / Lisa Fromm / Timo Denk / Nikola Kellner / Dirk Flemming / Paulina Fischer / Laurent Falquet / Otto Berninghausen / Roland Beckmann / Ed Hurt /
PubMed AbstractThe 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 linksEMBO Rep / PubMed:37921038 / PubMed Central
MethodsEM (single particle)
Resolution2.12 - 10.02 Å
Structure data

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

EMDB-17949, PDB-8puw:
Chaetomium thermophilum Las1-Grc3-complex
Method: EM (single particle) / Resolution: 3.01 Å

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

EMDB-17951, PDB-8pv2:
Chaetomium thermophilum pre-60S State 10 - pre-5S rotation with Ytm1-Erb1
Method: EM (single particle) / Resolution: 2.63 Å

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

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

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

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

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

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

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

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 molecule*YM

ChemComp-MG:
Unknown entry

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

Source
  • thermochaetoides thermophila dsm 1495 (fungus)
KeywordsRIBOSOME / biogenesis / pre-60S / 5S RNP

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