+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21564 | |||||||||
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Title | Structure of yeast RNase MRP holoenzyme | |||||||||
Map data | RNase MRP holoenzyme | |||||||||
Sample |
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Keywords | ribozyme / RNP / ribonucleoprotein / HYDROLASE | |||||||||
Function / homology | Function and homology information ribonuclease MRP activity / nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / plasmid partitioning / ribonuclease P / nuclease activity ...ribonuclease MRP activity / nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / plasmid partitioning / ribonuclease P / nuclease activity / ribonuclease P activity / rRNA primary transcript binding / tRNA 5'-leader removal / telomerase holoenzyme complex / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of 5.8S rRNA / tRNA processing / mRNA processing / rRNA processing / nucleolus / RNA binding / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Perederina A / Li D | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Cryo-EM structure of catalytic ribonucleoprotein complex RNase MRP. Authors: Anna Perederina / Di Li / Hyunwook Lee / Carol Bator / Igor Berezin / Susan L Hafenstein / Andrey S Krasilnikov / Abstract: RNase MRP is an essential eukaryotic ribonucleoprotein complex involved in the maturation of rRNA and the regulation of the cell cycle. RNase MRP is related to the ribozyme-based RNase P, but it has ...RNase MRP is an essential eukaryotic ribonucleoprotein complex involved in the maturation of rRNA and the regulation of the cell cycle. RNase MRP is related to the ribozyme-based RNase P, but it has evolved to have distinct cellular roles. We report a cryo-EM structure of the S. cerevisiae RNase MRP holoenzyme solved to 3.0 Å. We describe the structure of this 450 kDa complex, interactions between its components, and the organization of its catalytic RNA. We show that some of the RNase MRP proteins shared with RNase P undergo an unexpected RNA-driven remodeling that allows them to bind to divergent RNAs. Further, we reveal how this RNA-driven protein remodeling, acting together with the introduction of new auxiliary elements, results in the functional diversification of RNase MRP and its progenitor, RNase P, and demonstrate structural underpinnings of the acquisition of new functions by catalytic RNPs. | |||||||||
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_21564.map.gz | 475.3 MB | EMDB map data format | |
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Header (meta data) | emd-21564-v30.xml emd-21564.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
Images | emd_21564.png | 36.9 KB | ||
Filedesc metadata | emd-21564.cif.gz | 7.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21564 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21564 | HTTPS FTP |
-Validation report
Summary document | emd_21564_validation.pdf.gz | 584.3 KB | Display | EMDB validaton report |
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Full document | emd_21564_full_validation.pdf.gz | 583.9 KB | Display | |
Data in XML | emd_21564_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | emd_21564_validation.cif.gz | 9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21564 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21564 | HTTPS FTP |
-Related structure data
Related structure data | 6w6vMC 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_21564.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RNase MRP holoenzyme | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.665 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 : Ribonuclease MRP
+Supramolecule #1: Ribonuclease MRP
+Macromolecule #1: RNA component of RNase MRP NME1
+Macromolecule #2: Ribonucleases P/MRP protein subunit POP1
+Macromolecule #3: RNases MRP/P 32.9 kDa subunit
+Macromolecule #4: Ribonuclease P/MRP protein subunit POP5
+Macromolecule #5: Ribonucleases P/MRP protein subunit POP6
+Macromolecule #6: Ribonucleases P/MRP protein subunit POP7
+Macromolecule #7: Ribonucleases P/MRP protein subunit POP8
+Macromolecule #8: Ribonuclease P/MRP protein subunit RPP1
+Macromolecule #9: Ribonuclease MRP protein subunit SNM1
+Macromolecule #10: Ribonuclease MRP protein subunit RMP1
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | cell |
-Sample preparation
Buffer | pH: 8 |
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Grid | Pretreatment - Type: GLOW DISCHARGE / Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 39.0 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 |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 155205 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |