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- EMDB-33135: The intermediate pre-Tet-S1 state of wild-type Tetrahymena group ... -

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Basic information

Entry
Database: EMDB / ID: EMD-33135
TitleThe intermediate pre-Tet-S1 state of wild-type Tetrahymena group I intron with 6nt 3'/5'-exon
Map data
Sample
  • Complex: Co-transcriptional folded wild-type Tetrahymena group I intron with 6nt 3'/5'-exon
    • RNA: Co-transcriptional folded wild-type Tetrahymena group I intron with 6nt 3'/5'-exon
  • Ligand: MAGNESIUM ION
KeywordsCatalytic RNA / RNA
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.89 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)32070049 China
National Natural Science Foundation of China (NSFC)32222040 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 EF / Luo Y / Jiang L / Dong H / Wei X / Bujnicki JM / Su Z
History
DepositionMar 26, 2022-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33135.png

Downloads & links

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Map

FileDownload / File: emd_33135.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 224 pix.
= 190.4 Å		0.85 Å/pix.
x 224 pix.
= 190.4 Å		0.85 Å/pix.
x 224 pix.
= 190.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.06420729 - 0.14700773
Average (Standard dev.)0.0007521416 (±0.005262128)
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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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 6nt 3'/5'-exon
Components
  • Complex: Co-transcriptional folded wild-type Tetrahymena group I intron with 6nt 3'/5'-exon
    • RNA: Co-transcriptional folded wild-type Tetrahymena group I intron with 6nt 3'/5'-exon
  • Ligand: MAGNESIUM ION

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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 6nt 3'/5'-exon
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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

MacromoleculeName: Co-transcriptional folded wild-type Tetrahymena group I intron with 6nt 3'/5'-exon
type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 136.4815 KDa
SequenceString: CUCUCUAAAU AGCAAUAUUU ACCUUUGGAG GGAAAAGUUA UCAGGCAUGC ACCUGGUAGC UAGUCUUUAA ACCAAUAGAU UGCAUCGGU UUAAAAGGCA AGACCGUCAA AUUGCGGGAA AGGGGUCAAC AGCCGUUCAG UACCAAGUCU CAGGGGAAAC U UUGAGAUG ...String:
CUCUCUAAAU AGCAAUAUUU ACCUUUGGAG GGAAAAGUUA UCAGGCAUGC ACCUGGUAGC UAGUCUUUAA ACCAAUAGAU UGCAUCGGU UUAAAAGGCA AGACCGUCAA AUUGCGGGAA AGGGGUCAAC AGCCGUUCAG UACCAAGUCU CAGGGGAAAC U UUGAGAUG GCCUUGCAAA GGGUAUGGUA AUAAGCUGAC GGACAUGGUC CUAACCACGC AGCCAAGUCC UAAGUCAACA GA UCUUCUG UUGAUAUGGA UGCAGUUCAC AGACUAAAUG UCGGUCGGGG AAGAUGUAUU CUUCUCAUAA GAUAUAGUCG GAC CUCUCC UUAAUGGGAG CUAGCGGAUG AAGUGAUGCA ACACUGGAGC CGCUGGGAAC UAAUUUGUAU GCGAAAGUAU AUUG AUUAG UUUUGGAGUA CUCGUAAG

GENBANK: GENBANK: X54512.1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 28 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.36 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 79.3 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
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: 1-30 / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1643322
Startup modelType of model: EMDB MAP
EMDB ID:

31385

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 38028
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 6 / Avg.num./class: 39116 / Software - Name: RELION (ver. 3.1)

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Atomic model buiding 1

Initial modelPDB ID:

7ez0


Chain - Chain ID: N / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7xd4:
The intermediate pre-Tet-S1 state of wild-type Tetrahymena group I intron with 6nt 3'/5'-exon

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