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Open data
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Basic information
Entry | Database: PDB / ID: 6k0a | ||||||
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Title | cryo-EM structure of an archaeal Ribonuclease P | ||||||
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![]() | RNA BINDING PROTEIN/RNA / Ribonuclease P / RNA-protein complex / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | ![]() ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / ribonuclease P / box C/D sno(s)RNA binding / ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / box C/D snoRNP assembly / ribosome biogenesis ...ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / ribonuclease P / box C/D sno(s)RNA binding / ribonuclease P activity / tRNA 5'-leader removal / box C/D methylation guide snoRNP complex / box C/D snoRNP assembly / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / translation / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å | ||||||
![]() | Wan, F. / Lan, P. / Wu, J. / Lei, M. | ||||||
![]() | ![]() Title: Cryo-electron microscopy structure of an archaeal ribonuclease P holoenzyme. Authors: Futang Wan / Qianmin Wang / Jing Tan / Ming Tan / Juan Chen / Shaohua Shi / Pengfei Lan / Jian Wu / Ming Lei / ![]() Abstract: Ribonuclease P (RNase P) is an essential ribozyme responsible for tRNA 5' maturation. Here we report the cryo-EM structures of Methanocaldococcus jannaschii (Mja) RNase P holoenzyme alone and in ...Ribonuclease P (RNase P) is an essential ribozyme responsible for tRNA 5' maturation. Here we report the cryo-EM structures of Methanocaldococcus jannaschii (Mja) RNase P holoenzyme alone and in complex with a tRNA substrate at resolutions of 4.6 Å and 4.3 Å, respectively. The structures reveal that the subunits of MjaRNase P are strung together to organize the holoenzyme in a dimeric conformation required for efficient catalysis. The structures also show that archaeal RNase P is a functional chimera of bacterial and eukaryal RNase Ps that possesses bacterial-like two RNA-based anchors and a eukaryal-like protein-aided stabilization mechanism. The 3'-RCCA sequence of tRNA, which is a key recognition element for bacterial RNase P, is dispensable for tRNA recognition by MjaRNase P. The overall organization of MjaRNase P, particularly within the active site, is similar to those of bacterial and eukaryal RNase Ps, suggesting a universal catalytic mechanism for all RNase Ps. | ||||||
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 486.5 KB | Display | ![]() |
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PDB format | ![]() | 388.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 30036MC ![]() 9899 ![]() 9900C ![]() 6k0bC 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
-Ribonuclease P protein component ... , 4 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 15972.156 Da / Num. of mol.: 2 / Fragment: Pop5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: rnp2, MJ0494 / Plasmid: pETDuet / Production host: ![]() ![]() #2: Protein | Mass: 27394.783 Da / Num. of mol.: 2 / Fragment: Rpp30 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: rnp3, MJ1139 / Plasmid: pETDuet / Production host: ![]() ![]() #3: Protein | Mass: 10910.179 Da / Num. of mol.: 2 / Fragment: Rpp29 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: rnp1, MJ0464 / Plasmid: pETDuet / Production host: ![]() ![]() #4: Protein | Mass: 15610.048 Da / Num. of mol.: 2 / Fragment: Rpp21 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: rnp4, MJ0962 / Plasmid: pETDuet / Production host: ![]() ![]() |
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-Protein / RNA chain / Non-polymers , 3 types, 6 molecules IJXY![](data/chem/img/ZN.gif)
![](data/chem/img/ZN.gif)
#5: Protein | Mass: 12703.843 Da / Num. of mol.: 2 / Fragment: L7Ae Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Gene: rpl7ae, MJ1203 / Plasmid: pET28A / Production host: ![]() ![]() #6: RNA chain | Mass: 83581.586 Da / Num. of mol.: 2 / Fragment: RPR Source method: isolated from a genetically manipulated source Details: in vitro transcription Source: (gene. exp.) ![]() ![]() Production host: ![]() ![]() #7: Chemical | |
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-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: cryo-EM structure of an archaeal Ribonuclease P / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 8 |
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: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C2 (2 fold cyclic) |
3D reconstruction | Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84800 / Symmetry type: POINT |