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- EMDB-7809: Human nuclear exosome-MTR4 RNA complex - composite map after focu... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-7809 | |||||||||
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Title | Human nuclear exosome-MTR4 RNA complex - composite map after focused reconstruction | |||||||||
![]() | Composite map after focused reconstructions for a human nuclear exosome-RNA helicase complex | |||||||||
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Function / homology | ![]() DNA deamination / nucleolar exosome (RNase complex) / snRNA catabolic process / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Weick E-M / Lima CD | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex. Authors: Eva-Maria Weick / M Rhyan Puno / Kurt Januszyk / John C Zinder / Michael A DiMattia / Christopher D Lima / ![]() Abstract: The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4- ...The ribonucleolytic RNA exosome interacts with RNA helicases to degrade RNA. To understand how the 3' to 5' Mtr4 helicase engages RNA and the nuclear exosome, we reconstituted 14-subunit Mtr4-containing RNA exosomes from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and human and show that they unwind structured substrates to promote degradation. We loaded a human exosome with an optimized DNA-RNA chimera that stalls MTR4 during unwinding and determined its structure to an overall resolution of 3.45 Å by cryoelectron microscopy (cryo-EM). The structure reveals an RNA-engaged helicase atop the non-catalytic core, with RNA captured within the central channel and DIS3 exoribonuclease active site. MPP6 tethers MTR4 to the exosome through contacts to the RecA domains of MTR4. EXOSC10 remains bound to the core, but its catalytic module and cofactor C1D are displaced by RNA-engaged MTR4. Competition for the exosome core may ensure that RNA is committed to degradation by DIS3 when engaged by MTR4. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 5.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 36 KB 36 KB | Display Display | ![]() |
Images | ![]() | 52.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 326.5 KB | Display | ![]() |
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Full document | ![]() | 326.1 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 7.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6d6rMC ![]() 7808C ![]() 7810C ![]() 7812C ![]() 7813C ![]() 7814C ![]() 7815C ![]() 7818C ![]() 7819C ![]() 6d6qC C: citing same article ( M: atomic model generated by this map |
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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
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Composite map after focused reconstructions for a human nuclear exosome-RNA helicase complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 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 : Human nuclear exosome-MTR4 helicase captured after unwinding a DN...
+Supramolecule #1: Human nuclear exosome-MTR4 helicase captured after unwinding a DN...
+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 component 10
+Macromolecule #11: Exosome complex exonuclease RRP44
+Macromolecule #12: M-phase phosphoprotein 6
+Macromolecule #13: Exosome RNA helicase MTR4
+Macromolecule #14: RNA (5'-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3')
+Macromolecule #15: DNA/RNA (62-MER)
+Macromolecule #16: ZINC ION
+Macromolecule #17: MAGNESIUM ION
+Macromolecule #18: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 1.0 mg/mL | |||||||||||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/2 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.037 kPa | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV / Details: 30 sec wait time, 2.5 sec blot time. | |||||||||||||||||||||
Details | Sample was monodisperse upon elution from gel filtration prior to vitrification. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 1439 / Average electron dose: 85.23 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Particle selection | Number selected: 278185 | ||||||
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CTF correction | Software:
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Startup model | Type of model: NONE / Details: Ab initio model determination | ||||||
Initial angle assignment | Type: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 0.6.1) / Software - details: from 0.6.1 to 0.6.5 | ||||||
Final 3D classification | Number classes: 4 / Avg.num./class: 271036 / Software - Name: RELION (ver. 2.1b1) | ||||||
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1b1) | ||||||
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1b1) Details: Focused refinements with five strategies required to achieve final model Number images used: 122703 |
-Atomic model buiding 1
Details | Models were rebuilt manually using Coot, with real space refinement with local scaling followed by Phenix real space refinement with suboptimal global scaling. |
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Refinement | Space: REAL / Protocol: BACKBONE TRACE / Overall B value: 73.6 / Target criteria: Correlation coefficient |
Output model | ![]() PDB-6d6r: |