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- PDB-7xd6: The Tet-S2 state with a pseudoknotted 4-way junction of wild-type... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7xd6 | ||||||||||||||||||||||||
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Title | The Tet-S2 state with a pseudoknotted 4-way junction of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon | ||||||||||||||||||||||||
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![]() | RNA | ||||||||||||||||||||||||
Function / homology | SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100)![]() | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 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 | ![]() | 230.3 KB | Display | ![]() |
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PDB format | ![]() | 169.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1005.8 KB | Display | ![]() |
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Full document | ![]() | 1010.7 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 30.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 33137MC ![]() 7xd3C ![]() 7xd4C ![]() 7xd5C ![]() 7xd7C ![]() 8hd6C ![]() 8hd7C ![]() 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: 140071.703 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: RNA chain | Mass: 8014.804 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-SPD / | 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 wild-type Tetrahymena group I intron with 30nt 3'/5'-exon Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: synthetic construct (others) |
Buffer solution | pH: 7.9 |
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: 32 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: 15 / Used frames/image: 1-15 |
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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: 4188150 | ||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 494563 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 7EZ0 Pdb chain-ID: N / Accession code: 7EZ0 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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