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- EMDB-77868: Geobacillus stearothermophilus RNase P holoenzyme in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-77868
TitleGeobacillus stearothermophilus RNase P holoenzyme in complex with precursor tRNA at 2 mM MgCl2
Map data
Sample
  • Complex: ternary complex of Geobacillus stearothermophilus RNase P RNA, rnpA protein and pre-tRNA
    • RNA: RNA (417-MER)
    • Protein or peptide: Ribonuclease P protein component
    • RNA: RNA (89-MER)
    • RNA: RNA (5'-R(P*GP*GP*AP*UP*UP*UP*UP*CP*C)-3')
  • Ligand: MAGNESIUM ION
KeywordsRNase P / holoenzyme / pretRNA / enzyme substrate complex / ribonucleoprotein / catalytic RNA / RNA processing / cryoEM / RNA / HYDROLASE-RNA 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: 2.8 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: Geobacillus stearothermophilus RNase P holoenzyme in complex with precursor tRNA at 2 mM MgCl2
Authors: Frazao de Souza Degenhardt M / Stagno J / Wang Y-X
History
DepositionJul 1, 2026-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77868.png

Downloads & links

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Map

FileDownload / File: emd_77868.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.17 Å/pix.
x 320 pix.
= 374.784 Å		1.17 Å/pix.
x 320 pix.
= 374.784 Å		1.17 Å/pix.
x 320 pix.
= 374.784 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1712 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.14820123 - 0.45847934
Average (Standard dev.)-0.0000009207281 (±0.0056748805)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 374.784 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_77868_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_77868_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 : ternary complex of Geobacillus stearothermophilus RNase P RNA, rn...

EntireName: ternary complex of Geobacillus stearothermophilus RNase P RNA, rnpA protein and pre-tRNA
Components
  • Complex: ternary complex of Geobacillus stearothermophilus RNase P RNA, rnpA protein and pre-tRNA
    • RNA: RNA (417-MER)
    • Protein or peptide: Ribonuclease P protein component
    • RNA: RNA (89-MER)
    • RNA: RNA (5'-R(P*GP*GP*AP*UP*UP*UP*UP*CP*C)-3')
  • Ligand: MAGNESIUM ION

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Supramolecule #1: ternary complex of Geobacillus stearothermophilus RNase P RNA, rn...

SupramoleculeName: ternary complex of Geobacillus stearothermophilus RNase P RNA, rnpA protein and pre-tRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)

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Macromolecule #1: RNA (417-MER)

MacromoleculeName: 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 #3: RNA (89-MER)

MacromoleculeName: RNA (89-MER) / type: rna / ID: 3 / Number of copies: 1
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 36.247344 KDa
SequenceString:
GGGAUCCGGA UCCUUUUGGA UCCGUUAUCC CUUUCGCGGA AGUAGUUCAG UGGUAGAACA CCACCUUGCC AAGGUGGGGG UCGCGGGUU CGAGUCCCGU CUUCCGCUCC AAUA

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Macromolecule #4: RNA (5'-R(P*GP*GP*AP*UP*UP*UP*UP*CP*C)-3')

MacromoleculeName: RNA (5'-R(P*GP*GP*AP*UP*UP*UP*UP*CP*C)-3') / type: rna / ID: 4 / Number of copies: 1
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 2.809687 KDa
SequenceString:
GGAUUUUCC

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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 (E. coli)
SequenceString:
GMKKKYRIKK NEEFQEVFQQ GVSVANRQFV VYTLDRPEQP YFRIGLSVSK KLGKAVVRNR IKRYIRQCFL ELKEEVAPGK DYVIIARQP AAEMGYAEVK KSLIHVLRKA GGLKKEA

UniProtKB: Ribonuclease P protein component

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 24 / 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

Concentration2.2 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 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: PDB ENTRY
PDB model - PDB ID:

9owq

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 267589
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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