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- EMDB-37129: Cryo-EM structure of Hydrogenobacter thermophilus minimal protein... -

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Basic information

Entry
Database: EMDB / ID: EMD-37129
TitleCryo-EM structure of Hydrogenobacter thermophilus minimal protein-only RNase P (HARP) in complex with pre-tRNAs
Map data
Sample
  • Complex: Hydrogenobacter thermophilus RNA-free ribonuclease P, HARP, in complex with pre-tRNA
    • Protein or peptide: RNA-free ribonuclease P
    • RNA: Aquifex aeolicus pre-tRNAVal
  • Ligand: MAGNESIUM ION
Keywordspre-tRNA processing / tRNA / pre-tRNA complex / HYDROLASE-RNA COMPLEX / RNA-free ribonuclease P / ribonuclease P
Function / homologyRNA-free ribonuclease P / PINc domain ribonuclease / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / PIN-like domain superfamily / RNA-free ribonuclease P
Function and homology information
Biological speciesHydrogenobacter thermophilus (bacteria) / Hydrogenobacter thermophilus DSM 653 (bacteria) / Aquifex aeolicus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsTeramoto T / Adachi N / Yokogawa T / Koyasu T / Mayanagi K / Nakamura T / Senda T / Kakuta Y
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)21K06032 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101071 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101091 Japan
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis of transfer RNA processing by bacterial minimal RNase P.
Authors: Takamasa Teramoto / Takeshi Koyasu / Takashi Yokogawa / Naruhiko Adachi / Kouta Mayanagi / Takahiro Nakamura / Toshiya Senda / Yoshimitsu Kakuta /
Abstract: Precursor tRNAs (pre-tRNAs) require nucleolytic removal of 5'-leader and 3'-trailer sequences for maturation, which is essential for proper tRNA function. The endoribonuclease RNase P exists in ...Precursor tRNAs (pre-tRNAs) require nucleolytic removal of 5'-leader and 3'-trailer sequences for maturation, which is essential for proper tRNA function. The endoribonuclease RNase P exists in diverse forms, including RNA- and protein-based RNase P, and removes 5'-leader sequences from pre-tRNAs. Some bacteria and archaea possess a unique minimal protein-based RNase P enzyme, HARP, which forms dodecamers with twelve active sites. Here, we present cryogenic electron microscopy structures of HARP dodecamers complexed with five pre-tRNAs, and we show that HARP oligomerization enables specific recognition of the invariant distance between the acceptor stem 5'-end and the TψC-loop, functioning as a molecular ruler-a feature representing convergent evolution among RNase P enzymes. The HARP dodecamer uses only five active sites for 5'-leader cleavage, while we identify a 3'-trailer cleavage activity in the remaining seven sites. This elucidation reveals how small proteins evolve through oligomerization to adapt a pivotal biological function (5'-leader processing) and acquire a novel function (3'-trailer processing).
History
DepositionAug 9, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_37129.png

Downloads & links

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Map

FileDownload / File: emd_37129.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 400 pix.
= 348. Å		0.87 Å/pix.
x 400 pix.
= 348. Å		0.87 Å/pix.
x 400 pix.
= 348. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-0.026263667 - 0.043440536
Average (Standard dev.)0.000020241223 (±0.001298185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 348.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37129_msk_1.map
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Half map: #2

Fileemd_37129_half_map_1.map
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Half map: #1

Fileemd_37129_half_map_2.map
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Sample components

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Entire : Hydrogenobacter thermophilus RNA-free ribonuclease P, HARP, in co...

EntireName: Hydrogenobacter thermophilus RNA-free ribonuclease P, HARP, in complex with pre-tRNA
Components
  • Complex: Hydrogenobacter thermophilus RNA-free ribonuclease P, HARP, in complex with pre-tRNA
    • Protein or peptide: RNA-free ribonuclease P
    • RNA: Aquifex aeolicus pre-tRNAVal
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Hydrogenobacter thermophilus RNA-free ribonuclease P, HARP, in co...

SupramoleculeName: Hydrogenobacter thermophilus RNA-free ribonuclease P, HARP, in complex with pre-tRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Hydrogenobacter thermophilus (bacteria)

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Macromolecule #1: RNA-free ribonuclease P

MacromoleculeName: RNA-free ribonuclease P / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: ribonuclease P
Source (natural)Organism: Hydrogenobacter thermophilus DSM 653 (bacteria) / Strain: DSM 6534
Molecular weightTheoretical: 21.93909 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDTFVLDTSV FTNPDVYHQF EEDQLGAIEN FISLASHTNA NFFMPTSVYY EFTKMVSLGD LAPKFELVVR IRSPRKWGLM VPAEFLYEF IEEVRYRINK GLRIAEEHTK EAGKLAEEEV GRVVNRLREK YREALRAGII DSKEDVDVLL LSYELDAILV S GDEGLRKW ADRVGIKLID PKNLRYIMEN L

UniProtKB: RNA-free ribonuclease P

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Macromolecule #2: Aquifex aeolicus pre-tRNAVal

MacromoleculeName: Aquifex aeolicus pre-tRNAVal / type: rna / ID: 2 / Number of copies: 5
Source (natural)Organism: Aquifex aeolicus (bacteria)
Molecular weightTheoretical: 23.650148 KDa
SequenceString:
AAGGCGCGUA GCUCAGUAGG GAGAGCGCCG GCCCGACACG CCGGAGGUCG GGGGUUCAAG UCCCCCCGCG CCU

GENBANK: GENBANK: AE000657.1

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 5 / 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 mg/mL
BufferpH: 8
Component:
ConcentrationFormula
25.0 mMTris-HCl
100.0 mMNaCl
1.0 mMTCEP
5.0 mMMgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 11206 / Average electron dose: 50.0 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: 0.8 µm / Nominal magnification: 215000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1861832
CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: An ab initio model was generated using RELION3's own implementation of Stochastic Gradient Descent (SGD) algorithm and low-pass filtered to 60 A for use as an initial model for 3D classification.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 191471
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final 3D classificationSoftware - Name: RELION (ver. 4)

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