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Open data
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Basic information
Entry | Database: PDB / ID: 6ahr | ||||||
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Title | Cryo-EM structure of human Ribonuclease P | ||||||
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![]() | HYDROLASE/RNA / Ribonuclease P / RNA-protein complex / HYDROLASE-RNA complex | ||||||
Function / homology | ![]() multimeric ribonuclease P complex / ribonuclease MRP activity / 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 ...multimeric ribonuclease P complex / ribonuclease MRP activity / 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 | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.92 Å | ||||||
![]() | Wu, J. / Niu, S. / Tan, M. / Lan, P. / Lei, M. | ||||||
![]() | ![]() 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 |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 635.5 KB | Display | ![]() |
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PDB format | ![]() | 499.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1003.3 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 78.2 KB | Display | |
Data in CIF | ![]() | 121.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9626MC ![]() 9627C ![]() 6ahuC ![]() 6ahvC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 2 molecules BE
#2: Protein | Mass: 114896.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
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#5: Protein | Mass: 18844.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
-Ribonuclease P protein subunit ... , 8 types, 9 molecules CDFGHIJKL
#3: Protein | Mass: 31891.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() | ||||
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#4: Protein | Mass: 25474.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() | ||||
#6: Protein | Mass: 20659.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() | ||||
#7: Protein | Mass: 15672.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() | ||||
#8: Protein | Mass: 13707.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() | ||||
#9: Protein | Mass: 29364.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() #10: Protein | | Mass: 17596.068 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() #11: Protein | | Mass: 41884.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
-RNA chain / Non-polymers , 2 types, 2 molecules A![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#12: Chemical | ChemComp-ZN / |
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#1: RNA chain | Mass: 110244.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: cell / Source: (natural) ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: RNase P / Type: COMPLEX / Entity ID: #1-#11 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.5625 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 400198 / Symmetry type: POINT |