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- PDB-8kd9: Cryo-EM structure of Aquifex aeolicus minimal protein-only RNase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8kd9 | ||||||||||||
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Title | Cryo-EM structure of Aquifex aeolicus minimal protein-only RNase P (HARP) in complex with pre-tRNAs | ||||||||||||
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![]() | HYDROLASE-RNA COMPLEX / pre-tRNA processing / tRNA / pre-tRNA complex / RNA-free ribonuclease P / ribonuclease | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.87 Å | ||||||||||||
![]() | Teramoto, T. / Koyasu, T. / Mayanagi, K. / Yokogawa, T. / Adachi, N. / Nakamura, T. / Senda, T. / Kakuta, Y. | ||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 593.8 KB | Display | ![]() |
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PDB format | ![]() | 467.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 37128 M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 22242.473 Da / Num. of mol.: 12 / Mutation: C114S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: RNA chain | Mass: 23650.148 Da / Num. of mol.: 5 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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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 |
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Sample preparation
Component | Name: Aquifex aeolicus RNA-free ribonuclease P, HARP, in complex with pre-tRNA Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
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: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm |
Specimen holder | Cryogen: NITROGEN |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 8362 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4522335 | ||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 578312 / Symmetry type: POINT |