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- EMDB-74274: Cryo-EM structure of Geobacillus stearothermophilus RNase P holoe... -

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Basic information

Entry
Database: EMDB / ID: EMD-74274
TitleCryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 9
Map data
Sample
  • Complex: RNase P RNA and protein components in 1 mM Mg2+
    • RNA: RNase P RNA (417-MER)
    • Protein or peptide: Ribonuclease P protein component
  • Ligand: MAGNESIUM ION
Keywordsribozyme / 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
Ribonuclease P protein component
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsFrazao de Souza Degenhardt M / Stagno J / Wang Y-X
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 Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 9
Authors: Frazao de Souza Degenhardt M / Stagno J / Wang Y-X
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_74274.png

Downloads & links

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Map

FileDownload / File: emd_74274.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: 0.04
Minimum - Maximum-0.12971841 - 0.39009863
Average (Standard dev.)0.000025612944 (±0.0068270448)
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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Additional map: This volume is an EMReady-processed sharpened map derived...

Fileemd_74274_additional_1.map
AnnotationThis volume is an EMReady-processed sharpened map derived from the original cryo EM reconstruction, provided to enhance high-resolution feature interpretation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_74274_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_74274_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 : RNase P RNA and protein components in 1 mM Mg2+

EntireName: RNase P RNA and protein components in 1 mM Mg2+
Components
  • Complex: RNase P RNA and protein components in 1 mM Mg2+
    • RNA: RNase P RNA (417-MER)
    • Protein or peptide: Ribonuclease P protein component
  • Ligand: MAGNESIUM ION

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Supramolecule #1: RNase P RNA and protein components in 1 mM Mg2+

SupramoleculeName: RNase P RNA and protein components in 1 mM Mg2+ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 149.4 KDa

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

MacromoleculeName: RNase P RNA (417-MER) / 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: Ribonuclease P protein component

MacromoleculeName: Ribonuclease P protein component / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 13.456872 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GMKKKYRIKK NEEFQEVFQQ GVSVANRQFV VYTLDRPEQP YFRIGLSVSK KLGKAVVRNR IKRYIRQCFL ELKEEVAPGK DYVIIARQP AAEMGYAEVK KSLIHVLRKA GGLKKEA

UniProtKB: Ribonuclease P protein component

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 38 / 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

Concentration2.7 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 90990
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2a64


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: cross-correlation coefficient
Output model

PDB-9zih:
Cryo-EM structure of Geobacillus stearothermophilus RNase P holoenzyme in 1 mM Mg2+, conformer 9

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