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- PDB-9zfc: Cryo-EM structure of RNase P RNA from Geobacillus stearothermophi... -

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Basic information

Entry
Database: PDB / ID: 9zfc
TitleCryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 2
ComponentsRNase P RNA
KeywordsRNA / RNase P RNA / Geobacillus stearothermophilus / catalytic RNA / cryo-EM structure / conformational heterogeneity
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsDegenhardt, M.F.S. / 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: Nature / Year: 2026
Title: RNA catalysis emerges from dynamic structural ensembles.
Authors: Maximilia F S Degenhardt / Hermann F Degenhardt / Bapurao A Bhoge / Yun-Tzai Lee / Ping Yu / Jinwei Zhang / Justin C Deme / Jason R Stagno / Yun-Xing Wang /
Abstract: The dynamic interplay between RNA structure and its associated Mg ions is central to RNA function yet remains poorly understood at a near-atomic level. Here, using a heterogeneity-focused protocol ...The dynamic interplay between RNA structure and its associated Mg ions is central to RNA function yet remains poorly understood at a near-atomic level. Here, using a heterogeneity-focused protocol for cryo-electron microscopy data analysis of conformationally flexible RNA particles, we determined the structures of RNase P RNA ensembles composed of 76 coexisting active and inactive conformers that differ in a transient tertiary interaction that is critical for activity. The binding of the accessory protein does not change the local structure but induces thermodynamic allostery that enhances catalysis by altering the dynamics of the tertiary interaction. Four distinct classes of Mg ions have critical roles in the structure, dynamics and catalysis of the conformational ensembles. Together, these findings establish a new paradigm in which catalysis is regulated through multimodal communications coupled with the dynamics of RNA-Mg conformational ensembles, rather than a single static catalytic structure in a single action mode.
History
DepositionDec 1, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2026Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,13135
Polymers135,3041
Non-polymers82634
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain RNase P RNA


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: 143442
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 34 / 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: ribonuclease P RNA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.1355 MDa / Experimental value: NO
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Source (recombinant)Organism: in vitro transcription vector pT7-TP(deltai) (others)
Buffer solutionpH: 7.5 / Details: 25 mM Tris-HCl,pH 7.5, 100 mM NaCl, 1 mM MgCl2
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTris-HCl buffer1
2100 mMSodium chlorideNaCl1
31 mMMagnesium chlorideMgCl21
SpecimenConc.: 2.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The specimen consisted of monomeric RNase P RNA from Geobacillus stearothermophilus purified and prepared in buffer containing 1 mM Magnesium. Samples were applied directly to cryo-EM grids for vitrification
Specimen supportDetails: Glow-discharged Quantifoil R1.2/1.3 Au 300 mesh grids prepared on a Vitrobot. Grids were glow-discharged on both sides for 60 s at 25 mA prior to sample application. Sample concentration was ...Details: Glow-discharged Quantifoil R1.2/1.3 Au 300 mesh grids prepared on a Vitrobot. Grids were glow-discharged on both sides for 60 s at 25 mA prior to sample application. Sample concentration was 2.8 mg/mL. A 10 s wait time and 3 s blot with force 3 to 10 at 277 K were used during vitrification.
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K
Details: Grids were glow-discharged on both sides prior to vitrification. Vitrification was performed using a Vitrobot Mark IV with a 10s wait time, followed by a 3s blot and blot force 3 to 10

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 53 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 5 / Num. of real images: 78777
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.2_5419model refinement
5cryoSPARCCTF correction
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74471 / Symmetry type: POINT
Atomic model buildingB value: 61 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: maximization of map-to-model correlation
Atomic model buildingPDB-ID: 9OV3

9ov3


Pdb chain-ID: A / Accession code: 9OV3 / Chain residue range: 1-417 / Pdb chain residue range: 1-417 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310038
ELECTRON MICROSCOPYf_angle_d0.51315661
ELECTRON MICROSCOPYf_dihedral_angle_d24.5196209
ELECTRON MICROSCOPYf_chiral_restr0.0272085
ELECTRON MICROSCOPYf_plane_restr0.004417

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