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- PDB-8hd7: The intermediate pre-Tet-S1 state of G264A mutated Tetrahymena gr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8hd7 | ||||||||||||||||||||||||
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Title | The intermediate pre-Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside | ||||||||||||||||||||||||
![]() | The intermediate pre-Tet-S1 state molecule of co-transcriptional folded G264A mutant Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside | ||||||||||||||||||||||||
![]() | RNA / Catalytic RNA / G264A mutated Tetrahymena group I intron | ||||||||||||||||||||||||
Function / homology | SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100)![]() | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å | ||||||||||||||||||||||||
![]() | Luo, B. / Zhang, C. / Ling, X. / Mukherjee, S. / Jia, G. / Xie, J. / Jia, X. / Liu, L. / Baulin, E.F. / Luo, Y. ...Luo, B. / Zhang, C. / Ling, X. / Mukherjee, S. / Jia, G. / Xie, J. / Jia, X. / Liu, L. / Baulin, E.F. / Luo, Y. / Jiang, L. / Dong, H. / Wei, X. / Bujnicki, J.M. / Su, Z. | ||||||||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing Authors: Luo, B. / Zhang, C. / Ling, X. / Mukherjee, S. / Jia, G. / Xie, J. / Jia, X. / Liu, L. / Baulin, E.F. / Luo, Y. / Jiang, L. / Dong, H. / Wei, X. / Bujnicki, J.M. / Su, Z. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 210.9 KB | Display | ![]() |
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PDB format | ![]() | 154.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 20 KB | Display | |
Data in CIF | ![]() | 29.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 34671MC ![]() 7xd3C ![]() 7xd4C ![]() 7xd5C ![]() 7xd6C ![]() 7xd7C ![]() 8hd6C ![]() 8i7nC 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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1 |
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Components
#1: RNA chain | Mass: 135155.719 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
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#2: Chemical | ChemComp-SPD / | ||
#3: Chemical | ChemComp-MG / Has ligand of interest | N | |
-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: Co-transcriptional folded G264A mutated Tetrahymena group I intron with 6-nt 3'/5'-exon and 2-aminopurine nucleoside Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: synthetic construct (others) |
Buffer solution | pH: 7 |
Specimen | 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 R2/1 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 3700 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 79.3 K |
Image recording | Electron dose: 55 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 30 / Used frames/image: 1-30 |
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Processing
Software | Name: PHENIX / Version: 1.15.2_3472: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 4012136 | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111196 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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