+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4301 | |||||||||
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Title | Structure of the nuclear RNA exosome | |||||||||
Map data | Structure of the nuclear RNA exosome | |||||||||
Sample |
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Function / homology | Function and homology information nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear mRNA surveillance of mRNA 3'-end processing / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing ...nuclear mRNA surveillance of spliceosomal pre-mRNA splicing / nuclear mRNA surveillance of mRNA 3'-end processing / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing / nuclear polyadenylation-dependent CUT catabolic process / nuclear polyadenylation-dependent mRNA catabolic process / U5 snRNA 3'-end processing / regulatory ncRNA 3'-end processing / cytoplasmic exosome (RNase complex) / TRAMP-dependent tRNA surveillance pathway / RNA fragment catabolic process / CUT catabolic process / U4 snRNA 3'-end processing / nuclear polyadenylation-dependent rRNA catabolic process / nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay / : / poly(A)-dependent snoRNA 3'-end processing / exosome (RNase complex) / 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) / : / 3'-5' RNA helicase activity / rRNA catabolic process / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / histone mRNA catabolic process / nuclear mRNA surveillance / nonfunctional rRNA decay / rRNA primary transcript binding / poly(A) binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / poly(U) RNA binding / maturation of 5.8S rRNA / rRNA metabolic process / 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 / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / manganese ion binding / 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 / nucleotide binding / mRNA 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) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.6 Å | |||||||||
Authors | Schuller JM / Falk S / Conti E | |||||||||
Funding support | Belgium, 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4301.map.gz | 3.8 MB | EMDB map data format | |
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Header (meta data) | emd-4301-v30.xml emd-4301.xml | 32.2 KB 32.2 KB | Display Display | EMDB header |
Images | emd_4301.png | 520.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4301 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4301 | HTTPS FTP |
-Related structure data
Related structure data | 6fszMC 4302C 6ft6C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4301.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 38.4 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: PROJECTION MATCHING |
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Final angle assignment | Type: PROJECTION MATCHING |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22439 |