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- PDB-36uk: Geobacillus stearothermophilus RNase P holoenzyme in complex with... -

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Basic information

Entry
Database: PDB / ID: 36uk
TitleGeobacillus stearothermophilus RNase P holoenzyme in complex with precursor tRNA at 2 mM MgCl2
Components
  • RNA (417-MER)
  • RNA (5'-R(P*GP*GP*AP*UP*UP*UP*UP*CP*C)-3')
  • RNA (89-MER)
  • Ribonuclease P protein component
KeywordsHYDROLASE/RNA / RNase P / holoenzyme / pretRNA / enzyme substrate complex / ribonucleoprotein / catalytic RNA / RNA processing / cryoEM / RNA / HYDROLASE-RNA 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: 2.8 Å
AuthorsFrazao de Souza Degenhardt, M. / Stagno, J. / Wang, Y.-X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)ZIA BC 010379, ZIC BC 011535, ZIA BC 011669 United States
CitationJournal: To Be Published
Title: Geobacillus stearothermophilus RNase P holoenzyme in complex with precursor tRNA at 2 mM MgCl2
Authors: Frazao de Souza Degenhardt, M. / Stagno, J. / Wang, Y.-X.
History
DepositionJul 1, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / 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: RNA (417-MER)
B: Ribonuclease P protein component
C: RNA (89-MER)
E: RNA (5'-R(P*GP*GP*AP*UP*UP*UP*UP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,40128
Polymers187,8184
Non-polymers58324
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 RNA (417-MER)


Mass: 135304.172 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)
References: GenBank: M19021.1
#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 (E. coli) / References: UniProt: A0A150N245, ribonuclease P
#3: RNA chain RNA (89-MER)


Mass: 36247.344 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)
#4: RNA chain RNA (5'-R(P*GP*GP*AP*UP*UP*UP*UP*CP*C)-3')


Mass: 2809.687 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)
#5: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 24 / 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: ternary complex of Geobacillus stearothermophilus RNase P RNA, rnpA protein and pre-tRNA
Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Source (recombinant)Organism: in vitro transcription vector pT7-TP(deltai) (others)
Buffer solutionpH: 7.5
SpecimenConc.: 2.2 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: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: OTHER / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 267589 / Symmetry type: POINT
RefinementHighest resolution: 2.8 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313315
ELECTRON MICROSCOPYf_angle_d0.55320546
ELECTRON MICROSCOPYf_dihedral_angle_d24.8667793
ELECTRON MICROSCOPYf_chiral_restr0.0292711
ELECTRON MICROSCOPYf_plane_restr0.004679

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