+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9627 | |||||||||
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Title | Cryo-EM structure of human Ribonuclease P with mature tRNA | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Ribonuclease P / RNA-protein complex / HYDROLASE-RNA complex | |||||||||
Function / homology | Function and homology information multimeric ribonuclease P complex / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / tRNA decay / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing in the nucleus / tRNA processing ...multimeric ribonuclease P complex / nucleolar ribonuclease P complex / ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / tRNA decay / ribonuclease P activity / tRNA 5'-leader removal / tRNA processing in the nucleus / tRNA processing / centriolar satellite / Major pathway of rRNA processing in the nucleolus and cytosol / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / fibrillar center / rRNA processing / response to xenobiotic stimulus / intracellular membrane-bounded organelle / nucleolus / RNA binding / extracellular space / nucleoplasm / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.66 Å | |||||||||
Authors | Wu J / Niu S | |||||||||
Citation | Journal: Cell / Year: 2018 Title: Cryo-EM Structure of the Human Ribonuclease P Holoenzyme. Authors: Jian Wu / Shuangshuang Niu / Ming Tan / Chenhui Huang / Mingyue Li / Yang Song / Qianmin Wang / Juan Chen / Shaohua Shi / Pengfei Lan / Ming Lei / Abstract: Ribonuclease (RNase) P is a ubiquitous ribozyme that cleaves the 5' leader from precursor tRNAs. Here, we report cryo-electron microscopy structures of the human nuclear RNase P alone and in ...Ribonuclease (RNase) P is a ubiquitous ribozyme that cleaves the 5' leader from precursor tRNAs. Here, we report cryo-electron microscopy structures of the human nuclear RNase P alone and in complex with tRNA. Human RNase P is a large ribonucleoprotein complex that contains 10 protein components and one catalytic RNA. The protein components form an interlocked clamp that stabilizes the RNA in a conformation optimal for substrate binding. Human RNase P recognizes the tRNA using a double-anchor mechanism through both protein-RNA and RNA-RNA interactions. Structural comparison of the apo and tRNA-bound human RNase P reveals that binding of tRNA induces a local conformational change in the catalytic center, transforming the ribozyme into an active state. Our results also provide an evolutionary model depicting how auxiliary RNA elements in bacterial RNase P, essential for substrate binding, and catalysis, were replaced by the much more complex and multifunctional protein components in higher organisms. | |||||||||
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_9627.map.gz | 59.9 MB | EMDB map data format | |
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Header (meta data) | emd-9627-v30.xml emd-9627.xml | 23.8 KB 23.8 KB | Display Display | EMDB header |
Images | emd_9627.png | 152.6 KB | ||
Filedesc metadata | emd-9627.cif.gz | 7.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9627 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9627 | HTTPS FTP |
-Validation report
Summary document | emd_9627_validation.pdf.gz | 561.7 KB | Display | EMDB validaton report |
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Full document | emd_9627_full_validation.pdf.gz | 561.3 KB | Display | |
Data in XML | emd_9627_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_9627_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9627 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9627 | HTTPS FTP |
-Related structure data
Related structure data | 6ahuMC 9626C 6ahrC 6ahvC C: citing same article (ref.) M: atomic model generated by this map |
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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_9627.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-Sample components
+Entire : RNase P with tRNA
+Supramolecule #1: RNase P with tRNA
+Supramolecule #2: RNase P
+Supramolecule #3: RNA
+Macromolecule #1: H1 RNA
+Macromolecule #12: tRNA
+Macromolecule #2: Ribonucleases P/MRP protein subunit POP1
+Macromolecule #3: Ribonuclease P protein subunit p38
+Macromolecule #4: Ribonuclease P protein subunit p29
+Macromolecule #5: Ribonuclease P/MRP protein subunit POP5
+Macromolecule #6: Ribonuclease P protein subunit p25
+Macromolecule #7: Ribonuclease P protein subunit p20
+Macromolecule #8: Ribonuclease P protein subunit p14
+Macromolecule #9: Ribonuclease P protein subunit p30
+Macromolecule #10: Ribonuclease P protein subunit p21
+Macromolecule #11: Ribonuclease P protein subunit p40
+Macromolecule #13: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 287700 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |