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- PDB-9ows: Structure of Geobacillus stearothermophilus RNase P holoenzyme in... -

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Basic information

Entry
Database: PDB / ID: 9ows
TitleStructure of Geobacillus stearothermophilus RNase P holoenzyme in 5 mM Mg2+
Components
  • RNase P RNA (417-MER)
  • Ribonuclease P protein component
KeywordsRNA/Hydrolase / ribozyme / RNA / RNase P. / RNA-Hydrolase complex
Function / homology
Function and homology information


3'-tRNA processing endoribonuclease activity / ribonuclease P complex / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / tRNA binding
Similarity search - Function
Ribonuclease P / Ribonuclease P, conserved site / Ribonuclease P / Bacterial ribonuclease P protein component signature. / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA (> 100) / Ribonuclease P protein component
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsLee, Y.-T. / Stagno, J.R. / Wang, Y.-X.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)ZIA BC 011669 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)ZIA DK 075136 United States
CitationJournal: To Be Published
Title: Structures of RNase P ribozyme catalysis in apo and holo states
Authors: Lee, Y.-T. / Degenhardt, M.F.S. / Skeparnias, I. / Chen, S.-Y. / Bhoge, B.A. / Zhang, J. / Stagno, J.R. / Wang, Y.-X.
History
DepositionJun 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RNase P RNA (417-MER)
B: Ribonuclease P protein component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,29724
Polymers148,7622
Non-polymers53522
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain RNase P RNA (417-MER)


Mass: 135305.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Production host: in vitro transcription vector pT7-TP(deltai) (others)
#2: Protein Ribonuclease P protein component / RNase P protein / RNaseP protein / Protein C5


Mass: 13456.872 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: rnpA, B4114_2986 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A150N245, ribonuclease P
#3: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: RNase P RNA and protein components in 5 mM Mg2+ / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.1494 MDa / Experimental value: YES
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Source (recombinant)Organism: in vitro transcription vector pT7-TP(deltai) (others)
Buffer solutionpH: 7.5
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 4D-STEM / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 57 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 998359 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: cross-correlation coefficient
Atomic model buildingPDB-ID: 2A64

2a64


Accession code: 2A64 / Source name: PDB / Type: experimental model

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