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- EMDB-70940: Structure of Geobacillus stearothermophilus RNase P ribozyme in c... -

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Entry
Database: EMDB / ID: EMD-70940
TitleStructure of Geobacillus stearothermophilus RNase P ribozyme in complex with precursor tRNA with loop-back 5' leader
Map dataStructure of Geobacillus stearothermophilus RNase P ribozyme in complex with precursor tRNA with loop-back 5' leader
Sample
  • Complex: RNase P RNA component in complex with precursor tRNA in 5 mM Ca2+
    • RNA: RNase P RNA (417-MER)
    • RNA: precursor tRNA (109-MER)
  • Ligand: CALCIUM ION
Keywordsribozyme / RNA / RNase P.
Biological speciesGeobacillus stearothermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsLee Y-T / Stagno JR / Wang Y-X
Funding support United States, 2 items
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: Nat Commun / Year: 2026
Title: Structural basis for protein-free catalysis by ribonuclease P ribozyme.
Authors: Yun-Tzai Lee / Maximilia F S Degenhardt / Ilias Skeparnias / Szu-Yun Chen / Bapurao A Bhoge / Sergey G Tarasov / Marzena A Dyba / Jinwei Zhang / Jason R Stagno / Yun-Xing Wang /
Abstract: Ribonuclease P (RNase P) is an essential metallonuclease found in all three domains of life. However, the structural basis for the ancient RNase P RNA component acting alone as a ribozyme and ...Ribonuclease P (RNase P) is an essential metallonuclease found in all three domains of life. However, the structural basis for the ancient RNase P RNA component acting alone as a ribozyme and catalytic metal-ion chemistry remains unknown. We report a series of cryo-EM structures, at resolutions of 2.8-3.5 Å, of the Geobacillus stearothermophilus RNase P aporibozyme (apoE) in various states of the catalytic cycle. The formation of both the tetraloop/tetraloop-receptor interaction and the interdigitated double T-loop motif in the substrate-specificity domain facilitates substrate binding. The apoE uses two metal ions for catalysis, suggesting a catalytic mechanism and evolutionary importance of the RNase P ribozyme to function without its protein component. Together, our data portray the regulatory RNA-RNA interfaces, dynamic structures, and cation traffic that confer function to a trans-acting ribozyme.
History
DepositionJun 2, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70940.png

Downloads & links

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Map

FileDownload / File: emd_70940.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Geobacillus stearothermophilus RNase P ribozyme in complex with precursor tRNA with loop-back 5' leader
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 400 pix.
= 414.72 Å		1.04 Å/pix.
x 400 pix.
= 414.72 Å		1.04 Å/pix.
x 400 pix.
= 414.72 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0368 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028
Minimum - Maximum-0.16670887 - 0.57679665
Average (Standard dev.)0.00034498255 (±0.0069776513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 414.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_70940_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_70940_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : RNase P RNA component in complex with precursor tRNA in 5 mM Ca2+

EntireName: RNase P RNA component in complex with precursor tRNA in 5 mM Ca2+
Components
  • Complex: RNase P RNA component in complex with precursor tRNA in 5 mM Ca2+
    • RNA: RNase P RNA (417-MER)
    • RNA: precursor tRNA (109-MER)
  • Ligand: CALCIUM ION

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Supramolecule #1: RNase P RNA component in complex with precursor tRNA in 5 mM Ca2+

SupramoleculeName: RNase P RNA component in complex with precursor tRNA in 5 mM Ca2+
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 171.3 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: 135.304172 KDa
SequenceString: GUUAAUCAUG CUCGGGUAAU CGCUGCGGCC GGUUUCGGCC GUAGAGGAAA GUCCAUGCUC GCACGGUGCU GAGAUGCCCG UAGUGUUCG UGCCUAGCGA AUCCAUAAGC UAGGGCAGCC UGGCUUCGGC UGGGCUGACG GCGGGGAAAG AACCUACGUC C GGCUGGGA ...String:
GUUAAUCAUG CUCGGGUAAU CGCUGCGGCC GGUUUCGGCC GUAGAGGAAA GUCCAUGCUC GCACGGUGCU GAGAUGCCCG UAGUGUUCG UGCCUAGCGA AUCCAUAAGC UAGGGCAGCC UGGCUUCGGC 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: precursor tRNA (109-MER)

MacromoleculeName: precursor tRNA (109-MER) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 35.980219 KDa
SequenceString:
GGGAUCCGGA UCCUUUUGGA UCCGGAUCCC UUUCGCGGAA GUAGUUCAGU GGUAGAACAC CACCUUGCCA AGGUGGGGGU CGCGGGUUC GAGUCCCGUC UUCCGCUCCA AUA

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 31 / Formula: CA
Molecular weightTheoretical: 40.078 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

Concentration3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: 4D-STEM / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 248927
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.7.1)
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-9owq:
Structure of Geobacillus stearothermophilus RNase P ribozyme in complex with precursor tRNA with loop-back 5' leader

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