+Open data
-Basic information
Entry | Database: PDB / ID: 6fsz | ||||||
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Title | Structure of the nuclear RNA exosome | ||||||
Components |
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Keywords | RNA / RNA exosome / Ribosome / pre-ribosome / Mtr4 / Helicase | ||||||
Function / homology | Function and homology information nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / mRNA decay by 3' to 5' exoribonuclease / nuclear mRNA surveillance of mRNA 3'-end processing ...nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / mRNA decay by 3' to 5' exoribonuclease / nuclear mRNA surveillance of mRNA 3'-end processing / U1 snRNA 3'-end processing / regulatory ncRNA 3'-end processing / U5 snRNA 3'-end processing / RNA fragment catabolic process / nuclear polyadenylation-dependent CUT catabolic process / TRAMP-dependent tRNA surveillance pathway / cytoplasmic exosome (RNase complex) / CUT catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, non-stop decay / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / histone mRNA catabolic process / rRNA catabolic process / 3'-5' RNA helicase activity / nuclear mRNA surveillance / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / mRNA 3'-UTR AU-rich region binding / poly(A) binding / rRNA primary transcript binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / poly(U) RNA binding / nonfunctional rRNA decay / regulation of telomere maintenance / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / maturation of 5.8S rRNA / rRNA metabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / RNA processing / enzyme regulator activity / RNA endonuclease activity / mRNA processing / double-stranded RNA binding / manganese ion binding / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / double-stranded DNA binding / regulation of gene expression / endonuclease activity / tRNA binding / RNA helicase activity / single-stranded RNA binding / oxidoreductase activity / RNA helicase / mRNA binding / nucleotide binding / protein-containing complex binding / nucleolus / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||
Authors | Schuller, J.M. / Falk, S. / Conti, E. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Science / Year: 2018 Title: Structure of the nuclear exosome captured on a maturing preribosome. Authors: Jan Michael Schuller / Sebastian Falk / Lisa Fromm / Ed Hurt / Elena Conti / Abstract: The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex ...The RNA exosome complex processes and degrades a wide range of transcripts, including ribosomal RNAs (rRNAs). We used cryo-electron microscopy to visualize the yeast nuclear exosome holocomplex captured on a precursor large ribosomal subunit (pre-60) during 7-to-5.8 rRNA processing. The cofactors of the nuclear exosome are sandwiched between the ribonuclease core complex (Exo-10) and the remodeled "foot" structure of the pre-60 particle, which harbors the 5.8 rRNA precursor. The exosome-associated helicase Mtr4 recognizes the preribosomal substrate by docking to specific sites on the 25 rRNA, captures the 3' extension of the 5.8 rRNA, and channels it toward Exo-10. The structure elucidates how the exosome forms a structural and functional unit together with its massive pre-60 substrate to process rRNA during ribosome maturation. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6fsz.cif.gz | 868 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fsz.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6fsz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fsz_validation.pdf.gz | 879.3 KB | Display | wwPDB validaton report |
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Full document | 6fsz_full_validation.pdf.gz | 957.4 KB | Display | |
Data in XML | 6fsz_validation.xml.gz | 127.9 KB | Display | |
Data in CIF | 6fsz_validation.cif.gz | 200.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/6fsz ftp://data.pdbj.org/pub/pdb/validation_reports/fs/6fsz | HTTPS FTP |
-Related structure data
Related structure data | 4301MC 4302C 6ft6C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Exosome complex component ... , 9 types, 9 molecules AABBCCDDEEFFGGHHII
#2: Protein | Mass: 33799.590 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RRP45, YDR280W, D9954.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q05636 |
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#3: Protein | Mass: 27794.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SKI6, ECM20, RRP41, YGR195W, G7587 / Production host: Escherichia coli (E. coli) / References: UniProt: P46948 |
#4: Protein | Mass: 43977.805 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RRP43, YCR035C, YCR35C, YCR522 / Production host: Escherichia coli (E. coli) / References: UniProt: P25359 |
#5: Protein | Mass: 26913.988 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RRP46, YGR095C / Production host: Escherichia coli (E. coli) / References: UniProt: P53256 |
#6: Protein | Mass: 29294.398 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RRP42, YDL111C / Production host: Escherichia coli (E. coli) / References: UniProt: Q12277 |
#7: Protein | Mass: 27559.869 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: MTR3, YGR158C, G6676 / Production host: Escherichia coli (E. coli) / References: UniProt: P48240 |
#8: Protein | Mass: 26778.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RRP40, YOL142W / Production host: Escherichia coli (E. coli) / References: UniProt: Q08285 |
#9: Protein | Mass: 39714.445 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RRP4, YHR069C / Production host: Escherichia coli (E. coli) / References: UniProt: P38792 |
#10: Protein | Mass: 32805.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: CSL4, SKI4, YNL232W, N1154 / Production host: Escherichia coli (E. coli) / References: UniProt: P53859 |
-Exosome complex exonuclease ... , 2 types, 2 molecules JJKK
#11: Protein | Mass: 113983.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: DIS3, RRP44, YOL021C, O2197 / Production host: Escherichia coli (E. coli) References: UniProt: Q08162, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters |
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#12: Protein | Mass: 84159.586 Da / Num. of mol.: 1 / Mutation: D296N Source method: isolated from a genetically manipulated source Details: Inactive point mutant D296N Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: RRP6, UNC733, YOR001W / Production host: Escherichia coli (E. coli) References: UniProt: Q12149, Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters |
-Protein , 2 types, 2 molecules LLMM
#13: Protein | Mass: 21086.297 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: LRP1, RRP47, YC1D, YHR081W / Production host: Escherichia coli (E. coli) / References: UniProt: P38801 |
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#14: Protein | Mass: 122260.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MTR4, DOB1, YJL050W, J1158 / Production host: Escherichia coli (E. coli) / References: UniProt: P47047, RNA helicase |
-RNA chain / Protein/peptide , 2 types, 2 molecules 2NN
#15: Protein/peptide | Mass: 4101.711 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs ...Details: Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known,Residues labeled as unknown - belongs to Mpp6 but the sequence is not known Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast), (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MPP6, YNR024W, N3230 / Production host: Escherichia coli (E. coli) / References: UniProt: P53725 |
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#1: RNA chain | Mass: 7158.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE |
-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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 38.4 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22439 / Symmetry type: POINT |