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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: To Be Published
Title: Cryo-EM structure of Aquifex aeolicus 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_37128.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.79 Å
Density
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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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
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)

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