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- EMDB-37129: Cryo-EM structure of Hydrogenobacter thermophilus minimal protein... -
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Open data
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Basic information
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Title | Cryo-EM structure of Hydrogenobacter thermophilus minimal protein-only RNase P (HARP) in complex with pre-tRNAs | ||||||||||||
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![]() | pre-tRNA processing / tRNA / pre-tRNA complex / HYDROLASE-RNA COMPLEX / RNA-free ribonuclease P / ribonuclease P | ||||||||||||
Function / homology | RNA-free ribonuclease P / PINc domain ribonuclease / ribonuclease P / ribonuclease P activity / tRNA 5'-leader removal / PIN-like domain superfamily / RNA-free ribonuclease P![]() | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.19 Å | ||||||||||||
![]() | Teramoto T / Adachi N / Yokogawa T / Koyasu T / Mayanagi K / Nakamura T / Senda T / Kakuta Y | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | |||
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Header (meta data) | ![]() | |||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8kdaMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Hydrogenobacter thermophilus RNA-free ribonuclease P, HARP, in co...
Entire | Name: Hydrogenobacter thermophilus RNA-free ribonuclease P, HARP, in complex with pre-tRNA |
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Components |
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-Supramolecule #1: Hydrogenobacter thermophilus RNA-free ribonuclease P, HARP, in co...
Supramolecule | Name: Hydrogenobacter thermophilus RNA-free ribonuclease P, HARP, in complex with pre-tRNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: RNA-free ribonuclease P
Macromolecule | Name: RNA-free ribonuclease P / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: ribonuclease P |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 21.93909 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: Aquifex aeolicus pre-tRNAVal
Macromolecule | Name: Aquifex aeolicus pre-tRNAVal / type: rna / ID: 2 / Number of copies: 5 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.650148 KDa |
Sequence | String: AAGGCGCGUA GCUCAGUAGG GAGAGCGCCG GCCCGACACG CCGGAGGUCG GGGGUUCAAG UCCCCCCGCG CCU GENBANK: GENBANK: AE000657.1 |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2 mg/mL | ||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 | ||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number real images: 11206 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 215000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |