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- PDB-7xd7: The pre-Tet-C state of wild-type Tetrahymena group I intron with ... -

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Entry
Database: PDB / ID: 7xd7
TitleThe pre-Tet-C state of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon
ComponentsThe pre-Tet-C state molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon
KeywordsRNA / Catalytic RNA / wild-type Tetrahymena group I intron
Function / homologySPERMIDINE / : / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsLuo, 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
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA1301900 China
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
National Natural Science Foundation of China (NSFC)32070049 China
National Natural Science Foundation of China (NSFC)32070049 China
Polish National Science Centre2017/26/A/NZ1/01083 Poland
Polish National Science Centre2021/43/D/NZ1/03360 Poland
European Molecular Biology Organization (EMBO)ALTF 525-2022European Union
CitationJournal: 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
DepositionMar 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: The pre-Tet-C state molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,58531
Polymers130,7351
Non-polymers85030
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain The pre-Tet-C state molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon


Mass: 130735.078 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
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34) / Spermidine


Mass: 145.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H19N3
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 7.9
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen 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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: 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 holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 79.3 K
Image recordingElectron dose: 32 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 15 / Used frames/image: 1-15

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategory
1EMAN22.31particle selection
2EPU2.8image acquisition
4CTFFIND4.1.8CTF correction
5RELION3.1CTF correction
8UCSF Chimera1.14model fitting
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
14Coot0.9.1model refinement
15PHENIX1.15model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4188150
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 440735 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingPDB-ID: 7EZ0

7ez0


Pdb chain-ID: N / Accession code: 7EZ0 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00214046
ELECTRON MICROSCOPYf_angle_d0.76725123
ELECTRON MICROSCOPYf_dihedral_angle_d29.2825567
ELECTRON MICROSCOPYf_chiral_restr0.0292025
ELECTRON MICROSCOPYf_plane_restr0.003704

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