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- EMDB-9622: Cryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9622 | |||||||||
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Title | Cryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate | |||||||||
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Function / homology | ![]() nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / ribonuclease MRP activity / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / ribonuclease P / rRNA primary transcript binding / ribonuclease P activity ...nuclear-transcribed mRNA catabolic process, RNase MRP-dependent / intronic box C/D snoRNA processing / ribonuclease MRP activity / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / ribonuclease P / rRNA primary transcript binding / ribonuclease P activity / tRNA 5'-leader removal / telomerase holoenzyme complex / tRNA processing / maturation of 5.8S rRNA / rRNA processing / RNA binding / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.48 Å | |||||||||
![]() | Lan P / Tan M / Wu J / Lei M | |||||||||
![]() | ![]() Title: Structural insight into precursor tRNA processing by yeast ribonuclease P. Authors: Pengfei Lan / Ming Tan / Yuebin Zhang / Shuangshuang Niu / Juan Chen / Shaohua Shi / Shuwan Qiu / Xuejuan Wang / Xiangda Peng / Gang Cai / Hong Cheng / Jian Wu / Guohui Li / Ming Lei / ![]() Abstract: Ribonuclease P (RNase P) is a universal ribozyme responsible for processing the 5'-leader of pre-transfer RNA (pre-tRNA). Here, we report the 3.5-angstrom cryo-electron microscopy structures of ...Ribonuclease P (RNase P) is a universal ribozyme responsible for processing the 5'-leader of pre-transfer RNA (pre-tRNA). Here, we report the 3.5-angstrom cryo-electron microscopy structures of RNase P alone and in complex with pre-tRNA The protein components form a hook-shaped architecture that wraps around the RNA and stabilizes RNase P into a "measuring device" with two fixed anchors that recognize the L-shaped pre-tRNA. A universally conserved uridine nucleobase and phosphate backbone in the catalytic center together with the scissile phosphate and the O3' leaving group of pre-tRNA jointly coordinate two catalytic magnesium ions. Binding of pre-tRNA induces a conformational change in the catalytic center that is required for catalysis. Moreover, simulation analysis suggests a two-metal-ion S2 reaction pathway of pre-tRNA cleavage. These results not only reveal the architecture of yeast RNase P but also provide a molecular basis of how the 5'-leader of pre-tRNA is processed by eukaryotic RNase P. | |||||||||
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 | ![]() | 60 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23 KB 23 KB | Display Display | ![]() |
Images | ![]() | 67.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 498.4 KB | Display | ![]() |
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Full document | ![]() | 497.9 KB | Display | |
Data in XML | ![]() | 6.1 KB | Display | |
Data in CIF | ![]() | 6.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ah3MC ![]() 9616C ![]() 6agbC 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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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 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 : RNase P with pre-tRNA substrate
+Supramolecule #1: RNase P with pre-tRNA substrate
+Supramolecule #2: RNase P
+Supramolecule #3: pre-tRNA
+Macromolecule #1: Ribonuclease P RNA
+Macromolecule #11: pre-tRNA
+Macromolecule #2: Ribonucleases P/MRP protein subunit POP1
+Macromolecule #3: Ribonucleases P/MRP protein subunit POP3
+Macromolecule #4: RNases MRP/P 32.9 kDa subunit
+Macromolecule #5: Ribonuclease P/MRP protein subunit POP5
+Macromolecule #6: Ribonucleases P/MRP protein subunit POP6
+Macromolecule #7: Ribonucleases P/MRP protein subunit POP7
+Macromolecule #8: Ribonucleases P/MRP protein subunit POP8
+Macromolecule #9: Ribonuclease P/MRP protein subunit RPP1
+Macromolecule #10: Ribonuclease P protein subunit RPR2
+Macromolecule #12: MAGNESIUM ION
+Macromolecule #13: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5625 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 176896 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |