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Yorodumi- EMDB-37129: Cryo-EM structure of Hydrogenobacter thermophilus minimal protein... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37129 | ||||||||||||
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Title | Cryo-EM structure of Hydrogenobacter thermophilus minimal protein-only RNase P (HARP) in complex with pre-tRNAs | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | 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 Function and homology information | ||||||||||||
Biological species | Hydrogenobacter thermophilus (bacteria) / Hydrogenobacter thermophilus DSM 653 (bacteria) / Aquifex aeolicus (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.19 Å | ||||||||||||
Authors | Teramoto T / Adachi N / Yokogawa T / Koyasu T / Mayanagi K / Nakamura T / Senda T / Kakuta Y | ||||||||||||
Funding support | Japan, 3 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37129.map.gz | 228.5 MB | EMDB map data format | |
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Header (meta data) | emd-37129-v30.xml emd-37129.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
Images | emd_37129.png | 77.3 KB | ||
Masks | emd_37129_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-37129.cif.gz | 6 KB | ||
Others | emd_37129_half_map_1.map.gz emd_37129_half_map_2.map.gz | 194.6 MB 194.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37129 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37129 | HTTPS FTP |
-Validation report
Summary document | emd_37129_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_37129_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_37129_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | emd_37129_validation.cif.gz | 18.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37129 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37129 | HTTPS FTP |
-Related structure data
Related structure data | 8kdaMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_37129.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
-Mask #1
File | emd_37129_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_37129_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37129_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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: Hydrogenobacter thermophilus (bacteria) |
-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: Hydrogenobacter thermophilus DSM 653 (bacteria) / Strain: DSM 6534 |
Molecular weight | Theoretical: 21.93909 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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: Aquifex aeolicus (bacteria) |
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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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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: FIELD EMISSION GUN |
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 |