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- EMDB-37128: Cryo-EM structure of Aquifex aeolicus minimal protein-only RNase ... -

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Basic information

Entry
Database: EMDB / ID: EMD-37128
TitleCryo-EM structure of Aquifex aeolicus minimal protein-only RNase P (HARP) in complex with pre-tRNAs
Map data
Sample
  • Complex: Aquifex aeolicus RNA-free ribonuclease P, HARP, in complex with pre-tRNA
    • Protein or peptide: RNA-free ribonuclease P
    • RNA: Aquifex aeolicus pre-tRNAVal
Keywordspre-tRNA processing / tRNA / pre-tRNA complex / HYDROLASE-RNA COMPLEX / RNA-free ribonuclease P / ribonuclease
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 speciesAquifex aeolicus (bacteria) / Aquifex aeolicus VF5 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsTeramoto T / Koyasu T / Mayanagi K / Yokogawa T / Adachi N / 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_37128.png

Downloads & links

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Map

FileDownload / File: emd_37128.map.gz / Format: CCP4 / Size: 216 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.)
0.79 Å/pix.
x 384 pix.
= 303.36 Å		0.79 Å/pix.
x 384 pix.
= 303.36 Å		0.79 Å/pix.
x 384 pix.
= 303.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.79 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012
Minimum - Maximum-0.09170069 - 0.1577891
Average (Standard dev.)0.000036843947 (±0.0041310475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 303.36002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_37128_msk_1.map
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Half map: #2

Fileemd_37128_half_map_1.map
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Half map: #1

Fileemd_37128_half_map_2.map
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Sample components

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Entire : Aquifex aeolicus RNA-free ribonuclease P, HARP, in complex with p...

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

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Supramolecule #1: Aquifex aeolicus RNA-free ribonuclease P, HARP, in complex with p...

SupramoleculeName: Aquifex aeolicus RNA-free ribonuclease P, HARP, in complex with pre-tRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Aquifex aeolicus (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
Source (natural)Organism: Aquifex aeolicus VF5 (bacteria)
Molecular weightTheoretical: 22.242473 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDVFVLDTSV FTNPEIYRTF EEDQRGAMET FIHLALNSRA EFYMPTSVYT EMRKIMDVGE LWAEFEMVVK IRSPRRFQLT VPADFLYEF IEELRYRINK GLRIAEEHTR EASGSEDVGK LIARLREKYR EALRQGILDS KEDVDVLLLA YELDGVLVSA D EGLRTWAD KIGIKLIDPK NFKNILESLV RH

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 VF5 (bacteria)
Molecular weightTheoretical: 23.650148 KDa
SequenceString:
AAGGCGCGUA GCUCAGUAGG GAGAGCGCCG GCCCGACACG CCGGAGGUCG GGGGUUCAAG UCCCCCCGCG CCU

GENBANK: GENBANK: AE000657.1

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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: GOLD / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 8362 / Average electron dose: 55.0 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: 60000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 4522335
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / 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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number images used: 578312
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.3)
Final 3D classificationSoftware - Name: RELION (ver. 3.1.3)
FSC plot (resolution estimation)

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