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- EMDB-33137: The Tet-S2 state with a pseudoknotted 4-way junction of wild-type... -

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Basic information

Entry
Database: EMDB / ID: EMD-33137
TitleThe Tet-S2 state with a pseudoknotted 4-way junction of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon
Map data
Sample
  • Complex: Co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon
    • RNA: The Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (intron and 3'-exon)
    • RNA: The Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (5'-exon)
  • Ligand: MAGNESIUM ION
  • Ligand: SPERMIDINE
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsLuo B / Zhang C / Ling X / Mukherjee S / Jia G / Xie J / Jia X / Liu L / Baulin EF / Luo Y ...Luo B / Zhang C / Ling X / Mukherjee S / Jia G / Xie J / Jia X / Liu L / Baulin EF / Luo Y / Jiang L / Dong H / Wei X / Bujnicki JM / Su Z
Funding support China, Poland, European Union, 7 items
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)European 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 EF / Luo Y / Jiang L / Dong H / Wei X / Bujnicki JM / Su Z
History
DepositionMar 26, 2022-
Header (metadata) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateApr 5, 2023-
Current statusApr 5, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33137.png

Downloads & links

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Map

FileDownload / File: emd_33137.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.06713716 - 0.21414272
Average (Standard dev.)0.0005459729 (±0.005308185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 190.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_33137_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_33137_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Co-transcriptional folded wild-type Tetrahymena group I intron wi...

EntireName: Co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon
Components
  • Complex: Co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon
    • RNA: The Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (intron and 3'-exon)
    • RNA: The Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (5'-exon)
  • Ligand: MAGNESIUM ION
  • Ligand: SPERMIDINE

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Supramolecule #1: Co-transcriptional folded wild-type Tetrahymena group I intron wi...

SupramoleculeName: Co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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Macromolecule #1: The Tet-S2 state with a pseudoknotted 4-way junction molecule of ...

MacromoleculeName: The Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (intron and 3'-exon)
type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 140.071703 KDa
SequenceString: AUAGCAAUAU UUACCUUUGG AGGGAAAAGU UAUCAGGCAU GCACCUGGUA GCUAGUCUUU AAACCAAUAG AUUGCAUCGG UUUAAAAGG CAAGACCGUC AAAUUGCGGG AAAGGGGUCA ACAGCCGUUC AGUACCAAGU CUCAGGGGAA ACUUUGAGAU G GCCUUGCA ...String:
AUAGCAAUAU UUACCUUUGG AGGGAAAAGU UAUCAGGCAU GCACCUGGUA GCUAGUCUUU AAACCAAUAG AUUGCAUCGG UUUAAAAGG CAAGACCGUC AAAUUGCGGG AAAGGGGUCA ACAGCCGUUC AGUACCAAGU CUCAGGGGAA ACUUUGAGAU G GCCUUGCA AAGGGUAUGG UAAUAAGCUG ACGGACAUGG UCCUAACCAC GCAGCCAAGU CCUAAGUCAA CAGAUCUUCU GU UGAUAUG GAUGCAGUUC ACAGACUAAA UGUCGGUCGG GGAAGAUGUA UUCUUCUCAU AAGAUAUAGU CGGACCUCUC CUU AAUGGG AGCUAGCGGA UGAAGUGAUG CAACACUGGA GCCGCUGGGA ACUAAUUUGU AUGCGAAAGU AUAUUGAUUA GUUU UGGAG UACUCGUAAG GUAGCCAAAU GCCUCGUCA

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Macromolecule #2: The Tet-S2 state with a pseudoknotted 4-way junction molecule of ...

MacromoleculeName: The Tet-S2 state with a pseudoknotted 4-way junction molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (5'-exon)
type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 8.014804 KDa
SequenceString:
ACGGCGGGAG UAACUAUGAC UCUCU

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 28 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: SPERMIDINE

MacromoleculeName: SPERMIDINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: SPD
Molecular weightTheoretical: 145.246 Da
Chemical component information

ChemComp-SPD:
SPERMIDINE / Spermidine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.9
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00068 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.7 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 79.3 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-15 / Average electron dose: 32.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4188150
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ez0

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 494563

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Atomic model buiding 1

Initial modelChain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-7xd6:
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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