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- EMDB-74259: Cryo-EM structure of RNase P RNA from Geobacillus stearothermophi... -

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Basic information

Entry
Database: EMDB / ID: EMD-74259
TitleCryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 46
Map data
Sample
  • Organelle or cellular component: ribonuclease P RNA
    • RNA: RNase P RNA
  • Ligand: MAGNESIUM ION
KeywordsRNase P RNA / Geobacillus stearothermophilus / catalytic RNA / cryo-EM structure / conformational heterogeneity / RNA
Biological speciesGeobacillus stearothermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsDegenhardt MFS / Stagno J / Wang YX
Funding support United States, 1 items
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: Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 46
Authors: Degenhardt MFS / Stagno J / Wang YX
History
DepositionDec 3, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74259.png

Downloads & links

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Map

FileDownload / File: emd_74259.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 480 pix.
= 351.36 Å		0.73 Å/pix.
x 480 pix.
= 351.36 Å		0.73 Å/pix.
x 480 pix.
= 351.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.732 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.12877588 - 0.43342817
Average (Standard dev.)-0.00020797794 (±0.006476589)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 351.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_74259_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_74259_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ribonuclease P RNA

EntireName: ribonuclease P RNA
Components
  • Organelle or cellular component: ribonuclease P RNA
    • RNA: RNase P RNA
  • Ligand: MAGNESIUM ION

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Supramolecule #1: ribonuclease P RNA

SupramoleculeName: ribonuclease P RNA / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 135.5 KDa

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Macromolecule #1: RNase P RNA

MacromoleculeName: RNase P RNA / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 135.305156 KDa
SequenceString: GUUAAUCAUG CUCGGGUAAU CGCUGCGGCC GGUUUCGGCC GUAGAGGAAA GUCCAUGCUC GCACGGUGCU GAGAUGCCCG UAGUGUUCG UGCCUAGCGA AUCCAUAAGC UAGGGCAGCC UGGCUUUGGC UGGGCUGACG GCGGGGAAAG AACCUACGUC C GGCUGGGA ...String:
GUUAAUCAUG CUCGGGUAAU CGCUGCGGCC GGUUUCGGCC GUAGAGGAAA GUCCAUGCUC GCACGGUGCU GAGAUGCCCG UAGUGUUCG UGCCUAGCGA AUCCAUAAGC UAGGGCAGCC UGGCUUUGGC UGGGCUGACG GCGGGGAAAG AACCUACGUC C GGCUGGGA UAUGGUUCGA UUACCCUGAA AGUGCCACAG UGACGGAGCU CUAAGGGAAA CCUUAGAGGU GGAACGCGGU AA ACCCCAC GAGCGAGAAA CCCAAAUGAU GGUAGGGGCA CCUUCCCGAA GGAAAUGAAC GGAGGGAAGG ACAGGCGGCG CAU GCAGCC UGUAGAUAGA UGAUUACCGC CGGAGUACGA GGCGCAAAGC CGCUUGCAGU ACGAAGGUAC AGAACAUGGC UUAU AGAGC AUGAUUAACG UC

GENBANK: GENBANK: M19021.1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 39 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.8 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMTris-HClTris-HCl buffer
100.0 mMNaClSodium chloride
1.0 mMMgCl2Magnesium chloride

Details: 25 mM Tris-HCl,pH 7.5, 100 mM NaCl, 1 mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.02 kPa
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 ...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 2.7 mg/mL. A 10 s wait time and 3 s blot with force 3 to 10 at 277K were used during vitrification.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV
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 in air.
DetailsThe 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

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 80.0 K / Max: 100.0 K
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
SoftwareName: EPU (ver. 3.1)
Details: Automated EPU data collection was guided by ice-filter criteria, with manual selection of squares exhibiting uniform ice and no visible contamination.
DetailsThe alignment procedure was performed using the EPU software utilizing its autofocus and auto-tuning functions for initial microscope alignment. This was followed by manual fine-tuning adjustments of the beam shift, stigmation, and focus controls to ensure optimal image quality. Grid squares were screened systematically, ensuring the selection of areas with appropriate ice thickness and particle distribution. Image shift calibration and eucentric height adjustment were performed within EPU to maintain beam alignment during data acquisition
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 5 / Number real images: 78777 / Average exposure time: 2.5 sec. / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 21475910
Details: An iterative particle-cleaning workflow was applied, combining 2D classification and heterogeneous refinement with decoy classes to achieve exhaustive particle selection.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6)
Details: CTF correction was performed in cryoSPARC by patch-based motion correction followed by patch-based CTF estimation, providing per-particle local CTF parameters that were applied during 3D ...Details: CTF correction was performed in cryoSPARC by patch-based motion correction followed by patch-based CTF estimation, providing per-particle local CTF parameters that were applied during 3D refinement for phase and amplitude correction of all particles
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9ov3

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 152761
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9ov3


Chain - Chain ID: A / Chain - Residue range: 1-417 / Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: The initial model consisted of the complete biological assembly
SoftwareName: UCSF ChimeraX (ver. 1.9)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 57 / Target criteria: maximization of map-to-model correlation
Output model

PDB-9zi3:
Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 46

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