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- EMDB-70948: Structure of Geobacillus stearothermophilus RNase P holoenzyme in... -

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Basic information

Entry
Database: EMDB / ID: EMD-70948
TitleStructure of Geobacillus stearothermophilus RNase P holoenzyme in complex with the precursor tRNA with loop-back 5' leader (sub-conformation 2 of tRNA anticodon arm tilted)
Map dataStructure of Geobacillus stearothermophilus RNase P holoenzyme in complex with the precursor tRNA with loop-back 5' leader (sub-conformation 2 of tRNA anticodon arm tilted)
Sample
  • Complex: RNase P RNA component in 5 mM Ca2+
    • RNA: RNase P RNA (417-MER)
    • Protein or peptide: Ribonuclease P protein component
    • RNA: precursor tRNA (108-MER)
  • Ligand: CALCIUM 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: 2.69 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: To Be Published
Title: Structures of RNase P ribozyme catalysis in apo and holo states
Authors: Lee Y-T / Degenhardt MFS / Skeparnias I / Chen S-Y / Bhoge BA / Zhang J / Stagno JR / Wang Y-X
History
DepositionJun 2, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70948.png

Downloads & links

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Map

FileDownload / File: emd_70948.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of Geobacillus stearothermophilus RNase P holoenzyme in complex with the precursor tRNA with loop-back 5' leader (sub-conformation 2 of tRNA anticodon arm tilted)
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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0368 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.16709055 - 0.5322424
Average (Standard dev.)-0.00014235254 (±0.006802334)
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_70948_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_70948_half_map_2.map
AnnotationHalf Map B
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 component in 5 mM Ca2+

EntireName: RNase P RNA component in 5 mM Ca2+
Components
  • Complex: RNase P RNA component in 5 mM Ca2+
    • RNA: RNase P RNA (417-MER)
    • Protein or peptide: Ribonuclease P protein component
    • RNA: precursor tRNA (108-MER)
  • Ligand: CALCIUM ION

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Supramolecule #1: RNase P RNA component in 5 mM Ca2+

SupramoleculeName: RNase P RNA component in 5 mM Ca2+ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 185.3 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: 135.305156 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

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Macromolecule #3: precursor tRNA (108-MER)

MacromoleculeName: precursor tRNA (108-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 35.635012 KDa
SequenceString:
GGAUCCGGAU CCUUUUGGAU CCGGAUCCCU UUCGCGGAAG UAGUUCAGUG GUAGAACACC ACCUUGCCAA GGUGGGGGUC GCGGGUUCG AGUCCCGUCU UCCGCUCCAA UA

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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 #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 29 / 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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 483540
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-9owy:
Structure of Geobacillus stearothermophilus RNase P holoenzyme in complex with the precursor tRNA with loop-back 5' leader (sub-conformation 2 of tRNA anticodon arm tilted)

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