[English] 日本語
Yorodumi- EMDB-9622: Cryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9622 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of yeast Ribonuclease P with pre-tRNA substrate | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
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 / ribonuclease P / rRNA primary transcript binding / ribonuclease P 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 / ribonuclease P / rRNA primary transcript binding / ribonuclease P activity / telomerase holoenzyme complex / tRNA 5'-leader removal / tRNA processing / maturation of 5.8S rRNA / Major pathway of rRNA processing in the nucleolus and cytosol / rRNA processing / RNA binding / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (brewer's yeast) / Saccharomyces cerevisiae S288c (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.48 Å | |||||||||
Authors | Lan P / Tan M / Wu J / Lei M | |||||||||
Citation | Journal: Science / Year: 2018 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9622.map.gz | 60 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-9622-v30.xml emd-9622.xml | 23 KB 23 KB | Display Display | EMDB header |
Images | emd_9622.png | 67.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9622 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9622 | HTTPS FTP |
-Related structure data
Related structure data | 6ah3MC 9616C 6agbC 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_9622.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.32 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-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 |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.5625 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
---|---|
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 176896 |