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Yorodumi- PDB-7xd5: The Tet-S2 state of wild-type Tetrahymena group I intron with 30n... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7xd5 | ||||||||||||||||||||||||
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Title | The Tet-S2 state of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon | ||||||||||||||||||||||||
Components |
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Keywords | RNA / Catalytic RNA | ||||||||||||||||||||||||
Function / homology | SPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100) Function and homology information | ||||||||||||||||||||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å | ||||||||||||||||||||||||
Authors | 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 | China, Poland, European Union, 7items
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Citation | Journal: Nat Catal / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7xd5.cif.gz | 203.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7xd5.ent.gz | 150.8 KB | Display | PDB format |
PDBx/mmJSON format | 7xd5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xd/7xd5 ftp://data.pdbj.org/pub/pdb/validation_reports/xd/7xd5 | HTTPS FTP |
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-Related structure data
Related structure data | 33136MC 7xd3C 7xd4C 7xd6C 7xd7C 8hd6C 8hd7C 8i7nC 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: RNA chain | Mass: 129222.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Production host: synthetic construct (others) / References: GenBank: 10832 | ||
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#2: RNA chain | Mass: 1789.085 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetrahymena thermophila (eukaryote) / Production host: synthetic construct (others) | ||
#3: Chemical | ChemComp-SPD / | ||
#4: 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 |
-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: Tetrahymena thermophila (eukaryote) |
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 |
-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 FIELDBright-field microscopy / 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 |
-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: 1088579 / 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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