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Yorodumi- PDB-8kda: Cryo-EM structure of Hydrogenobacter thermophilus minimal protein... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8kda | ||||||||||||
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Title | Cryo-EM structure of Hydrogenobacter thermophilus minimal protein-only RNase P (HARP) in complex with pre-tRNAs | ||||||||||||
Components |
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Keywords | HYDROLASE/RNA / pre-tRNA processing / tRNA / pre-tRNA complex / HYDROLASE-RNA COMPLEX / RNA-free ribonuclease P / ribonuclease P | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Hydrogenobacter thermophilus DSM 653 (bacteria) Aquifex aeolicus (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / 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, 3items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8kda.cif.gz | 639.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8kda.ent.gz | 517.9 KB | Display | PDB format |
PDBx/mmJSON format | 8kda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8kda_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8kda_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8kda_validation.xml.gz | 75.5 KB | Display | |
Data in CIF | 8kda_validation.cif.gz | 117.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kd/8kda ftp://data.pdbj.org/pub/pdb/validation_reports/kd/8kda | HTTPS FTP |
-Related structure data
Related structure data | 37129MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 21939.090 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hydrogenobacter thermophilus DSM 653 (bacteria) Strain: DSM 6534 / Gene: HTH_1307 / Production host: Escherichia coli (E. coli) / References: UniProt: D3DIV8, ribonuclease P #2: RNA chain | Mass: 23650.148 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) Aquifex aeolicus (bacteria) / References: GenBank: 6626248 #3: Chemical | ChemComp-MG / Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Hydrogenobacter thermophilus RNA-free ribonuclease P, HARP, in complex with pre-tRNA Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Hydrogenobacter thermophilus (bacteria) | ||||||||||||||||||||
Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 215000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 11206 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1861832 | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 191471 / Symmetry type: POINT |