+
Open data
-
Basic information
Entry | Database: PDB / ID: 6k0b | ||||||
---|---|---|---|---|---|---|---|
Title | cryo-EM structure of archaeal Ribonuclease P with mature tRNA | ||||||
![]() |
| ||||||
![]() | RNA BINDING PROTEIN/RNA / Ribonuclease P / RNA-protein complex / RNA BINDING PROTEIN-RNA complex | ||||||
Function / homology | ![]() multimeric ribonuclease P complex / 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 ...multimeric ribonuclease P complex / 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 / maturation of LSU-rRNA / maturation of SSU-rRNA / small-subunit processome / mRNA splicing, via spliceosome / rRNA processing / cytosolic large ribosomal subunit / rRNA binding / structural constituent of ribosome / translation / zinc ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 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. | ||||||
History |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 571.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 450.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 775.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 808.5 KB | Display | |
Data in XML | ![]() | 52.7 KB | Display | |
Data in CIF | ![]() | 84.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9900MC ![]() 6k0aC C: citing same article ( M: map data used to model this data |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
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 Variant: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 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 Variant: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 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 Variant: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 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 Variant: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Plasmid: pETDuet / Production host: ![]() ![]() |
---|
-RNA chain , 2 types, 4 molecules UVXY
#6: RNA chain | Mass: 26613.838 Da / Num. of mol.: 2 / Fragment: tRNA Source method: isolated from a genetically manipulated source Details: in vitro transcription / Source: (gene. exp.) ![]() ![]() ![]() ![]() #7: 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: ![]() ![]() |
---|
-Protein / Non-polymers , 2 types, 4 molecules IJ![](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 Variant: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440 Plasmid: pET28A / Production host: ![]() ![]() #8: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-
Sample preparation
Component | Name: cryo-EM structure of archaeal Ribonuclease P with mature tRNA Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT |
---|---|
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 |
-
Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 1.32 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-
Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
Symmetry | Point symmetry: C2 (2 fold cyclic) |
3D reconstruction | Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150000 / Symmetry type: POINT |