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- PDB-6k0a: cryo-EM structure of an archaeal Ribonuclease P -

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Basic information

Entry
Database: PDB / ID: 6k0a
Titlecryo-EM structure of an archaeal Ribonuclease P
Components
  • (Ribonuclease P protein component ...) x 4
  • 50S ribosomal protein L7AeRibosome
  • RPR
KeywordsRNA BINDING PROTEIN/RNA / Ribonuclease P / RNA-protein complex / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


ribonuclease MRP complex / ribonuclease P RNA binding / ribonuclease P complex / ribonuclease P / box C/D sno(s)RNA binding / box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / 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 / box C/D methylation guide snoRNP complex / ribonuclease P activity / tRNA 5'-leader removal / box C/D snoRNP assembly / ribosome biogenesis / rRNA binding / ribosome / structural constituent of ribosome / translation / zinc ion binding / cytoplasm
Similarity search - Function
Ribonuclease P protein subunit Rnp2, archaea / Ribonuclease P subunit RNP4 / Ribonuclease P, protein component 3, archaeal / Ribonuclease P protein subunit RNP1 / RNase P subunit Pop5/Rpp14/Rnp2-like / Ribonuclease P/MRP subunit Rpp29 / RNase P subunit Pop5/Rpp14/Rnp2-like domain superfamily / Rpp14/Pop5 family / RNase P subunit p30 / Ribonuclease P subunit, Rpr2/Snm1/Rpp21 ...Ribonuclease P protein subunit Rnp2, archaea / Ribonuclease P subunit RNP4 / Ribonuclease P, protein component 3, archaeal / Ribonuclease P protein subunit RNP1 / RNase P subunit Pop5/Rpp14/Rnp2-like / Ribonuclease P/MRP subunit Rpp29 / RNase P subunit Pop5/Rpp14/Rnp2-like domain superfamily / Rpp14/Pop5 family / RNase P subunit p30 / Ribonuclease P subunit, Rpr2/Snm1/Rpp21 / RNase P subunit p30 / RNAse P Rpr2/Rpp21/SNM1 subunit domain / Ribonuclease P protein subunit Rpp29/RNP1 / Ribonuclease P/MRP subunit Rpp29 superfamily / Ribonuclease P/MRP, subunit p29 / A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins. / Rof/RNase P-like / Polymerase/histidinol phosphatase-like / Ribosomal protein L7Ae, archaea / Ribosomal protein L7Ae conserved site / Ribosomal protein L7Ae signature. / Ribosomal protein L7Ae/L8/Nhp2 family / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Large ribosomal subunit protein eL8 / Ribonuclease P protein component 1 / Ribonuclease P protein component 2 / Ribonuclease P protein component 4 / Ribonuclease P protein component 3
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsWan, F. / Lan, P. / Wu, J. / Lei, M.
CitationJournal: Nat Commun / Year: 2019
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
DepositionMay 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name
Revision 1.2Nov 6, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.3May 20, 2020Group: Database references / Category: pdbx_database_related
Revision 1.4Dec 21, 2022Group: Database references / Category: database_2 / pdbx_database_related
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
A: Ribonuclease P protein component 2
C: Ribonuclease P protein component 3
E: Ribonuclease P protein component 1
G: Ribonuclease P protein component 4
I: 50S ribosomal protein L7Ae
X: RPR
B: Ribonuclease P protein component 2
D: Ribonuclease P protein component 3
F: Ribonuclease P protein component 1
H: Ribonuclease P protein component 4
J: 50S ribosomal protein L7Ae
Y: RPR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,47614
Polymers332,34512
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area31260 Å2
ΔGint-210 kcal/mol
Surface area146860 Å2

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Components

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Ribonuclease P protein component ... , 4 types, 8 molecules ABCDEFGH

#1: Protein Ribonuclease P protein component 2 / / RNase P component 2 / Pop5


Mass: 15972.156 Da / Num. of mol.: 2 / Fragment: Pop5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: rnp2, MJ0494 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57917, ribonuclease P
#2: Protein Ribonuclease P protein component 3 / / RNase P component 3 / Rpp30


Mass: 27394.783 Da / Num. of mol.: 2 / Fragment: Rpp30
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: rnp3, MJ1139 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q58539, ribonuclease P
#3: Protein Ribonuclease P protein component 1 / / RNase P component 1 / Rpp29


Mass: 10910.179 Da / Num. of mol.: 2 / Fragment: Rpp29
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: rnp1, MJ0464 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57903, ribonuclease P
#4: Protein Ribonuclease P protein component 4 / / RNase P component 4 / Rpp21


Mass: 15610.048 Da / Num. of mol.: 2 / Fragment: Rpp21
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: rnp4, MJ0962 / Plasmid: pETDuet / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q58372, ribonuclease P

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Protein / RNA chain / Non-polymers , 3 types, 6 molecules IJXY

#5: Protein 50S ribosomal protein L7Ae / Ribosome / Ribosomal protein L8e


Mass: 12703.843 Da / Num. of mol.: 2 / Fragment: L7Ae
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: rpl7ae, MJ1203 / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P54066
#6: RNA chain RPR


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.) Methanocaldococcus jannaschii (archaea)
Production host: Escherichia coli (E. coli)
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: cryo-EM structure of an archaeal Ribonuclease P / Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84800 / Symmetry type: POINT

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