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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-4301 | |||||||||
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Title | Structure of the nuclear RNA exosome | |||||||||
![]() | Structure of the nuclear RNA exosome | |||||||||
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![]() | RNA exosome / Ribosome / pre-ribosome / Mtr4 / Helicase / RNA | |||||||||
Function / homology | ![]() nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear mRNA surveillance of mRNA 3'-end processing / 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 / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process ...nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear mRNA surveillance of mRNA 3'-end processing / 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 / mRNA decay by 3' to 5' exoribonuclease / nuclear polyadenylation-dependent CUT catabolic process / regulatory ncRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / CUT catabolic process / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / U1 snRNA 3'-end processing / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / cytoplasmic exosome (RNase complex) / nuclear exosome (RNase complex) / nuclear-transcribed mRNA catabolic process, non-stop decay / poly(A)-dependent snoRNA 3'-end processing / U4 snRNA 3'-end processing / : / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / : / 3'-5' RNA helicase activity / histone mRNA catabolic process / nuclear mRNA surveillance / rRNA catabolic process / nonfunctional rRNA decay / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / poly(A) binding / rRNA primary transcript binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / poly(U) RNA binding / RNA catabolic process / rRNA metabolic process / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / regulation of gene expression / double-stranded DNA binding / endonuclease activity / tRNA binding / RNA helicase activity / oxidoreductase activity / single-stranded RNA binding / RNA helicase / nucleotide binding / mRNA binding / protein-containing complex binding / nucleolus / ATP hydrolysis activity / mitochondrion / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
![]() | Schuller JM / Falk S | |||||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 3.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 33 KB 33 KB | Display Display | ![]() |
Images | ![]() | 520.6 KB | ||
Filedesc metadata | ![]() | 9.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 211.2 KB | Display | ![]() |
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Full document | ![]() | 210.4 KB | Display | |
Data in XML | ![]() | 7.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6fszMC ![]() 4302C ![]() 6ft6C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Structure of the nuclear RNA exosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Nuclear RNA exosome
+Supramolecule #1: Nuclear RNA exosome
+Supramolecule #2: Nuclear RNA exosome
+Supramolecule #3: nucleic acid
+Macromolecule #1: RNA (5'-R(P*AP*AP*AP*AP*UP*UP*UP*AP*AP*AP*UP*UP*UP*UP*UP*UP*UP*UP...
+Macromolecule #2: Exosome complex component RRP45
+Macromolecule #3: Exosome complex component SKI6
+Macromolecule #4: Exosome complex component RRP43
+Macromolecule #5: Exosome complex component RRP46
+Macromolecule #6: Exosome complex component RRP42
+Macromolecule #7: Exosome complex component MTR3
+Macromolecule #8: Exosome complex component RRP40
+Macromolecule #9: Exosome complex component RRP4
+Macromolecule #10: Exosome complex component CSL4
+Macromolecule #11: Exosome complex exonuclease DIS3
+Macromolecule #12: Exosome complex exonuclease RRP6
+Macromolecule #13: Exosome complex protein LRP1
+Macromolecule #14: ATP-dependent RNA helicase DOB1
+Macromolecule #15: M-phase phosphoprotein 6 homolog,M-phase phosphoprotein 6 homolog...
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 38.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22439 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |