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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: To Be Published
Title: Cryo-EM structure of Hydrogenobacter thermophilus minimal protein-only RNase P (HARP) in complex with pre-tRNAs
Authors: Teramoto T / Koyasu T / Yokogawa T / Adachi N / Mayanagi K / Nakamura T / Senda T / Kakuta Y
History
DepositionAug 9, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: PDBj / Status: Released

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Structure visualization

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)
Voxel sizeX=Y=Z: 0.87 Å
Density
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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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
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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