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- EMDB-26638: E.coli RNaseP Holoenzyme with Mg2+ -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-26638
TitleE.coli RNaseP Holoenzyme with Mg2+
Map data
Sample
  • Complex: E.coli RNase P holoenzyme with Mg2+
    • Protein or peptide: Ribonuclease P protein component
    • RNA: RNase P RNA
  • Ligand: MAGNESIUM ION
Keywordsribozyme / protein-RNA complex / divalent ion / RNA / HYDROLASE-RNA complex
Function / homology
Function and homology information


ribonuclease P complex / 3'-tRNA processing endoribonuclease activity / 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 speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHuang W / Taylor DJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM133841 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural and mechanistic basis for recognition of alternative tRNA precursor substrates by bacterial ribonuclease P.
Authors: Jiaqiang Zhu / Wei Huang / Jing Zhao / Loc Huynh / Derek J Taylor / Michael E Harris /
Abstract: Binding of precursor tRNAs (ptRNAs) by bacterial ribonuclease P (RNase P) involves an encounter complex (ES) that isomerizes to a catalytic conformation (ES*). However, the structures of ...Binding of precursor tRNAs (ptRNAs) by bacterial ribonuclease P (RNase P) involves an encounter complex (ES) that isomerizes to a catalytic conformation (ES*). However, the structures of intermediates and the conformational changes that occur during binding are poorly understood. Here, we show that pairing between the 5' leader and 3'RCCA extending the acceptor stem of ptRNA inhibits ES* formation. Cryo-electron microscopy single particle analysis reveals a dynamic enzyme that becomes ordered upon formation of ES* in which extended acceptor stem pairing is unwound. Comparisons of structures with alternative ptRNAs reveals that once unwinding is completed RNase P primarily uses stacking interactions and shape complementarity to accommodate alternative sequences at its cleavage site. Our study reveals active site interactions and conformational changes that drive molecular recognition by RNase P and lays the foundation for understanding how binding interactions are linked to helix unwinding and catalysis.
History
DepositionApr 12, 2022-
Header (metadata) releaseSep 28, 2022-
Map releaseSep 28, 2022-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26638.png

Downloads & links

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Map

FileDownload / File: emd_26638.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 368 pix.
= 446.458 Å		1.21 Å/pix.
x 368 pix.
= 446.458 Å		1.21 Å/pix.
x 368 pix.
= 446.458 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2132 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.167
Minimum - Maximum-0.17746264 - 0.9361245
Average (Standard dev.)-0.00008117448 (±0.012077808)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 446.45758 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : E.coli RNase P holoenzyme with Mg2+

EntireName: E.coli RNase P holoenzyme with Mg2+
Components
  • Complex: E.coli RNase P holoenzyme with Mg2+
    • Protein or peptide: Ribonuclease P protein component
    • RNA: RNase P RNA
  • Ligand: MAGNESIUM ION

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Supramolecule #1: E.coli RNase P holoenzyme with Mg2+

SupramoleculeName: E.coli RNase P holoenzyme with Mg2+ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Ribonuclease P protein component

MacromoleculeName: Ribonuclease P protein component / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 13.818256 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MVKLAFPREL RLLTPSQFTF VFQQPQRAGT PQITILGRLN SLGHPRIGLT VAKKNVRRAH ERNRIKRLTR ESFRLRQHEL PAMDFVVVA KKGVADLDNR ALSEALEKLW RRHCRLARGS

UniProtKB: Ribonuclease P protein component

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Macromolecule #2: RNase P RNA

MacromoleculeName: RNase P RNA / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 122.108414 KDa
SequenceString: GAAGCUGACC AGACAGUCGC CGCUUCGUCG UCGUCCUCUU CGGGGGAGAC GGGCGGAGGG GAGGAAAGUC CGGGCUCCAU AGGGCAGGG UGCCAGGUAA CGCCUGGGGG GGAAACCCAC GACCAGUGCA ACAGAGAGCA AACCGCCGAU GGCCCGCGCA A GCGGGAUC ...String:
GAAGCUGACC AGACAGUCGC CGCUUCGUCG UCGUCCUCUU CGGGGGAGAC GGGCGGAGGG GAGGAAAGUC CGGGCUCCAU AGGGCAGGG UGCCAGGUAA CGCCUGGGGG GGAAACCCAC GACCAGUGCA ACAGAGAGCA AACCGCCGAU GGCCCGCGCA A GCGGGAUC AGGUAAGGGU GAAAGGGUGC GGUAAGAGCG CACCGCGCGG CUGGUAACAG UCCGUGGCAC GGUAAACUCC AC CCGGAGC AAGGCCAAAU AGGGGUUCAU AAGGUACGGC CCGUACUGAA CCCGGGUAGG CUGCUUGAGC CAGUGAGCGA UUG CUGGCC UAGAUGAAUG ACUGUCCACG ACAGAACCCG GCUUAUCGGU CAGUUUCCCU

GENBANK: GENBANK: CP053595.1

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Macromolecule #3: MAGNESIUM ION

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

BufferpH: 7.1
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 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: OTHER / Details: ab initio map generated by cryosparc
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 538466
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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