+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7808 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human nuclear exosome-MTR4 RNA complex - overall reconstruction | |||||||||
Map data | Overall reconstruction for human nuclear exosome-MTR4 helicase complex | |||||||||
Sample |
| |||||||||
Keywords | RNA exosome / RNA degradation / ribonuclease / helicase / SF2 / RNA-protein complex / translocase / nuclear / HYDROLASE | |||||||||
Function / homology | Function and homology information DNA deamination / nucleolar exosome (RNase complex) / snRNA catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent CUT catabolic process / positive regulation of mRNA cis splicing, via spliceosome / mRNA decay by 3' to 5' exoribonuclease ...DNA deamination / nucleolar exosome (RNase complex) / snRNA catabolic process / nuclear polyadenylation-dependent snoRNA catabolic process / nuclear polyadenylation-dependent snRNA catabolic process / TRAMP complex / nuclear polyadenylation-dependent antisense transcript catabolic process / nuclear polyadenylation-dependent CUT catabolic process / positive regulation of mRNA cis splicing, via spliceosome / mRNA decay by 3' to 5' exoribonuclease / regulation of telomerase RNA localization to Cajal body / TRAMP-dependent tRNA surveillance pathway / CUT catabolic process / RNA exonuclease activity / exosome (RNase complex) / nuclear polyadenylation-dependent rRNA catabolic process / cytoplasmic exosome (RNase complex) / U1 snRNA 3'-end processing / U5 snRNA 3'-end processing / nuclear exosome (RNase complex) / U4 snRNA 3'-end processing / 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 / mRNA 3'-UTR AU-rich region binding / 7S RNA binding / isotype switching / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / RNA catabolic process / telomerase RNA binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / KSRP (KHSRP) binds and destabilizes mRNA / nuclear-transcribed mRNA catabolic process / nuclear chromosome / maturation of 5.8S rRNA / mRNA catabolic process / negative regulation of telomere maintenance via telomerase / Major pathway of rRNA processing in the nucleolus and cytosol / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / guanyl-nucleotide exchange factor activity / small-subunit processome / euchromatin / fibrillar center / mRNA splicing, via spliceosome / rRNA processing / chromosome / ribosomal small subunit biogenesis / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / positive regulation of cell growth / endonuclease activity / defense response to virus / RNA polymerase II-specific DNA-binding transcription factor binding / RNA helicase activity / single-stranded RNA binding / RNA helicase / nuclear speck / immune response / intracellular membrane-bounded organelle / DNA repair / nucleotide binding / DNA damage response / nucleolus / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.45 Å | |||||||||
Authors | Weick E-M / Lima CD | |||||||||
Funding support | United States, 2 items
| |||||||||
Citation | Journal: Cell / Year: 2018 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_7808.map.gz | 15.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-7808-v30.xml emd-7808.xml | 36.2 KB 36.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7808_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_7808.png | 46.2 KB | ||
Filedesc metadata | emd-7808.cif.gz | 11 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7808 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7808 | HTTPS FTP |
-Validation report
Summary document | emd_7808_validation.pdf.gz | 389.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_7808_full_validation.pdf.gz | 388.7 KB | Display | |
Data in XML | emd_7808_validation.xml.gz | 13.6 KB | Display | |
Data in CIF | emd_7808_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7808 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7808 | HTTPS FTP |
-Related structure data
Related structure data | 6d6qMC 7809C 7810C 7812C 7813C 7814C 7815C 7818C 7819C 6d6rC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_7808.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Overall reconstruction for human nuclear exosome-MTR4 helicase complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-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: MAGNESIUM ION
+Macromolecule #17: ZINC ION
+Macromolecule #18: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.0 mg/mL | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| |||||||||||||||||||||
Grid | Model: Quantifoil R2/2 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / 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. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
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 |
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 |
+Image processing
-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. |
---|---|
Refinement | Space: REAL / Protocol: BACKBONE TRACE / Overall B value: 73.6 / Target criteria: Correlation coefficient |
Output model | PDB-6d6q: |