+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0127 | |||||||||
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Title | Human nuclear RNA exosome EXO-14 complex | |||||||||
Map data | Cryo-EM reconstruction of the human nuclear RNA exosome EXO-14 complex | |||||||||
Sample |
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Biological species | synthetic construct (others) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.25 Å | |||||||||
Authors | Gerlach P / Schuller JM / Falk S / Basquin J / Conti E | |||||||||
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_0127.map.gz | 5.4 MB | EMDB map data format | |
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Header (meta data) | emd-0127-v30.xml emd-0127.xml | 28.6 KB 28.6 KB | Display Display | EMDB header |
Images | emd_0127.png | 55.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0127 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0127 | HTTPS FTP |
-Validation report
Summary document | emd_0127_validation.pdf.gz | 213.8 KB | Display | EMDB validaton report |
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Full document | emd_0127_full_validation.pdf.gz | 212.9 KB | Display | |
Data in XML | emd_0127_validation.xml.gz | 5.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0127 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0127 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0127.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-14 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: Human nuclear RNA exosome EXO-14 complex
+Supramolecule #3: Human nuclear RNA exosome EXO-14 complex
+Macromolecule #1: EXOSC9
+Macromolecule #2: EXOSC4
+Macromolecule #3: EXOSC8
+Macromolecule #4: EXOSC5
+Macromolecule #5: EXOSC7
+Macromolecule #6: EXOSC6
+Macromolecule #7: EXOSC3
+Macromolecule #8: EXOSC2
+Macromolecule #9: EXOSC1
+Macromolecule #10: DIS3
+Macromolecule #11: MPP6
+Macromolecule #12: EXOSC10
+Macromolecule #13: C1D
+Macromolecule #14: MTR4
+Macromolecule #15: 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 |