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- PDB-7xd3: The relaxed pre-Tet-S1 state of wild-type Tetrahymena group I int... -

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Basic information

Entry
Database: PDB / ID: 7xd3
TitleThe relaxed pre-Tet-S1 state of wild-type Tetrahymena group I intron with 6nt 3'/5'-exon
ComponentsThe relaxed pre-Tet-S1 state molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 6nt 3'/5'-exon
KeywordsRNA / Catalytic RNA / Tetrahymena group I intron
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesTetrahymena thermophila (eukaryote)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.05 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)32222040 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
Revision 1.1Jun 26, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin
Item: _em_3d_fitting_list.initial_refinement_model_id / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: The relaxed pre-Tet-S1 state molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 6nt 3'/5'-exon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,14329
Polymers137,4621
Non-polymers68128
Water00
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 relaxed pre-Tet-S1 state molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 6nt 3'/5'-exon


Mass: 137462.094 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.: 28 / Source method: obtained synthetically / Formula: Mg
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 6nt 3'/5'-exon
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
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: COPPER / 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 FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2500 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: 61 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: 30 / Used frames/image: 1-30

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
EM software
IDNameVersionCategory
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
14PHENIX1.15model refinement
15Coot0.8.7model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1643322
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 44326 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
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_d0.00214655
ELECTRON MICROSCOPYf_angle_d0.77126224
ELECTRON MICROSCOPYf_dihedral_angle_d19.4545809
ELECTRON MICROSCOPYf_chiral_restr0.0282115
ELECTRON MICROSCOPYf_plane_restr0.003735

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