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Yorodumi- PDB-8pv6: Chaetomium thermophilum pre-60S State 3 - post-5S rotation with R... -
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-Basic information
Entry | Database: PDB / ID: 8pv6 | ||||||
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Title | Chaetomium thermophilum pre-60S State 3 - post-5S rotation with Rix1 complex with Foot - composite structure | ||||||
Components |
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Keywords | RIBOSOME / biogenesis / pre-60S / 5S RNP | ||||||
Function / homology | Function and homology information 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 Similarity search - Function | ||||||
Biological species | Thermochaetoides thermophila DSM 1495 (fungus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å | ||||||
Authors | Thoms, M. / Cheng, J. / Denk, T. / Berninghausen, O. / Beckmann, R. | ||||||
Funding support | European Union, 1items
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Citation | Journal: EMBO Rep / Year: 2023 Title: Structural insights into coordinating 5S RNP rotation with ITS2 pre-RNA processing during ribosome formation. 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 / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pv6.cif.gz | 3.9 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8pv6.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8pv6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/8pv6 ftp://data.pdbj.org/pub/pdb/validation_reports/pv/8pv6 | HTTPS FTP |
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-Related structure data
Related structure data | 17955MC 8ptwC 8puwC 8pv1C 8pv2C 8pv3C 8pv4C 8pv5C 8pv7C 8pv8C 8pvkC 8pvlC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 4 types, 4 molecules C1C2C3C4
#1: RNA chain | Mass: 1080783.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) |
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#2: RNA chain | Mass: 50147.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: GenBank: MT316345.1 |
#3: RNA chain | Mass: 52085.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: GenBank: 1373509168 |
#4: RNA chain | Mass: 38312.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) |
-Protein , 13 types, 13 molecules CFCICJCLCNCOCRCbChCzLJLhLr
#5: Protein | Mass: 30526.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S616 |
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#7: Protein | Mass: 45884.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S1H0 |
#8: Protein | Mass: 77167.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0SHX6 |
#10: Protein | Mass: 61479.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0SEW3 |
#12: Protein | Mass: 26468.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S683 |
#13: Protein | Mass: 13262.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0SHK0 |
#15: Protein | Mass: 86963.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S215 |
#19: Protein | Mass: 13710.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0SB32 |
#22: Protein | Mass: 57620.664 Da / Num. of mol.: 1 / Mutation: E117D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermochaetoides thermophila DSM 1495 (fungus) Gene: CTHT_0055700 Production host: Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0SC29 |
#23: Protein | Mass: 14710.419 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0SCP3 |
#31: Protein | Mass: 20119.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0SHQ2 |
#54: Protein | Mass: 105169.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S0D7, dolichyl-diphosphooligosaccharide-protein glycotransferase |
#61: Protein | Mass: 24055.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S4Z9 |
-Nucleolar GTP-binding protein ... , 2 types, 2 molecules CHCd
#6: Protein | Mass: 75621.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S8F1 |
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#20: Protein | Mass: 70313.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0SBX1 |
-Ribosome biogenesis protein ... , 3 types, 3 molecules CKCQCe
#9: Protein | Mass: 29724.580 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S081 |
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#14: Protein | Mass: 26434.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S497 |
#21: Protein | Mass: 50981.254 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S495 |
+60S ribosomal protein ... , 28 types, 29 molecules CMLFLALBLCLDLELGLHLKLLLMLOLPLSLTLULVLXLYLZLaLbLcLeLfLiLkLp
-Pre-rRNA-processing protein ... , 3 types, 5 molecules CSCTCUCVCW
#16: Protein | Mass: 37439.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: P0CT45 | ||
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#17: Protein | Mass: 47627.816 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S1T5 #18: Protein | Mass: 84849.219 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S5R0 |
-Ribosomal protein ... , 6 types, 6 molecules LNLQLRLgLjLl
#35: Protein | Mass: 24307.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0RZ88 |
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#38: Protein | Mass: 24195.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S9B5 |
#39: Protein | Mass: 317092.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S9T3 |
#53: Protein | Mass: 13492.993 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0SFN0 |
#56: Protein | Mass: 10660.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0S101 |
#58: Protein | Mass: 6297.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: Q2H9R2 |
-Putative 60S ribosomal ... , 2 types, 2 molecules LdLq
#50: Protein | Mass: 13872.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0SD68 |
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#60: Protein | Mass: 15960.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Thermochaetoides thermophila DSM 1495 (fungus) References: UniProt: G0SHJ6 |
-Non-polymers , 4 types, 14 molecules
#62: Chemical | #63: Chemical | #64: Chemical | ChemComp-ZN / #65: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Source (natural) |
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Source (recombinant) | Organism: Thermochaetoides thermophila DSM 1495 (fungus) | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 400 nm |
Image recording | Electron dose: 46 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 25753 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.38 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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