+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0128 | ||||||||||||||||||
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Title | Human nuclear RNA exosome EXO-10-MPP6 complex | ||||||||||||||||||
Map data | Cryo-EM reconstruction of the human nuclear RNA exosome EXO-10-MPP6 complex | ||||||||||||||||||
Sample |
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Keywords | nuclear exosome / RNA decay / cryoEM / hEXO-10 / hDIS3 / hMPP6 / RNA BINDING PROTEIN | ||||||||||||||||||
Function / homology | Function and homology information DNA deamination / nucleolar exosome (RNase complex) / nuclear mRNA surveillance of mRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U5 snRNA 3'-end processing / CUT catabolic process / cytoplasmic exosome (RNase complex) / exosome (RNase complex) ...DNA deamination / nucleolar exosome (RNase complex) / nuclear mRNA surveillance of mRNA 3'-end processing / mRNA decay by 3' to 5' exoribonuclease / U1 snRNA 3'-end processing / TRAMP-dependent tRNA surveillance pathway / U5 snRNA 3'-end processing / CUT catabolic process / cytoplasmic exosome (RNase complex) / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / U4 snRNA 3'-end processing / nuclear exosome (RNase complex) / poly(A)-dependent snoRNA 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) / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / ATF4 activates genes in response to endoplasmic reticulum stress / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / histone mRNA catabolic process / nuclear mRNA surveillance / positive regulation of isotype switching / rRNA catabolic process / 7S RNA binding / mRNA 3'-UTR AU-rich region binding / isotype switching / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / KSRP (KHSRP) binds and destabilizes mRNA / nuclear chromosome / maturation of 5.8S rRNA / mRNA catabolic process / nuclear-transcribed mRNA catabolic process / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / guanyl-nucleotide exchange factor activity / euchromatin / fibrillar center / rRNA processing / chromosome / positive regulation of cell growth / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / endonuclease activity / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / immune response / intracellular membrane-bounded organelle / nucleolus / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||||||||||||||
Authors | Gerlach P / Schuller JM / Falk S / Basquin J / Conti E | ||||||||||||||||||
Funding support | 5 items
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Citation | Journal: Elife / Year: 2018 Title: Distinct and evolutionary conserved structural features of the human nuclear exosome complex. Authors: Piotr Gerlach / Jan M Schuller / Fabien Bonneau / Jérôme Basquin / Peter Reichelt / Sebastian Falk / Elena Conti / Abstract: The nuclear RNA exosome complex mediates the processing of structured RNAs and the decay of aberrant non-coding RNAs, an important function particularly in human cells. Most mechanistic studies to ...The nuclear RNA exosome complex mediates the processing of structured RNAs and the decay of aberrant non-coding RNAs, an important function particularly in human cells. Most mechanistic studies to date have focused on the yeast system. Here, we reconstituted and studied the properties of a recombinant 14-subunit human nuclear exosome complex. In biochemical assays, the human exosome embeds a longer RNA channel than its yeast counterpart. The 3.8 Å resolution cryo-EM structure of the core complex bound to a single-stranded RNA reveals that the RNA channel path is formed by two distinct features of the hDIS3 exoribonuclease: an open conformation and a domain organization more similar to bacterial RNase II than to yeast Rrp44. The cryo-EM structure of the holo-complex shows how obligate nuclear cofactors position the hMTR4 helicase at the entrance of the core complex, suggesting a striking structural conservation from lower to higher eukaryotes. | ||||||||||||||||||
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_0128.map.gz | 4.8 MB | EMDB map data format | |
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Header (meta data) | emd-0128-v30.xml emd-0128.xml | 28.1 KB 28.1 KB | Display Display | EMDB header |
Images | emd_0128.png | 78.6 KB | ||
Filedesc metadata | emd-0128.cif.gz | 8.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0128 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0128 | HTTPS FTP |
-Validation report
Summary document | emd_0128_validation.pdf.gz | 228.5 KB | Display | EMDB validaton report |
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Full document | emd_0128_full_validation.pdf.gz | 227.6 KB | Display | |
Data in XML | emd_0128_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0128 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0128 | HTTPS FTP |
-Related structure data
Related structure data | 6h25MC 0127C C: citing same article (ref.) M: atomic model generated by this map |
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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_0128.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM reconstruction of the human nuclear RNA exosome EXO-10-MPP6 complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Human nuclear RNA exosome EXO-14 complex
+Supramolecule #1: Human nuclear RNA exosome EXO-14 complex
+Supramolecule #2: exosome complex
+Supramolecule #3: U44 ssRNA
+Macromolecule #1: Exosome complex component RRP45
+Macromolecule #2: Exosome complex component RRP41
+Macromolecule #3: Exosome complex component RRP43
+Macromolecule #4: Exosome complex component RRP46
+Macromolecule #5: Exosome complex component RRP42
+Macromolecule #6: Exosome complex component MTR3
+Macromolecule #7: Exosome complex component RRP40
+Macromolecule #8: Exosome complex component RRP4
+Macromolecule #9: Exosome complex component CSL4
+Macromolecule #10: Exosome complex exonuclease RRP44
+Macromolecule #11: M-phase phosphoprotein 6
+Macromolecule #12: U44 ssRNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL | ||||||||
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Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 8047 / Average electron dose: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |