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- EMDB-33136: The Tet-S2 state of wild-type Tetrahymena group I intron with 30n... -

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Basic information

Entry
Database: EMDB / ID: EMD-33136
TitleThe Tet-S2 state 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 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 molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (5'-exon)
  • Ligand: SPERMIDINE
  • Ligand: MAGNESIUM ION
KeywordsCatalytic RNA / RNA
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)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) releaseApr 5, 2023-
Map releaseApr 5, 2023-
UpdateJun 26, 2024-
Current statusJun 26, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33136.png

Downloads & links

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Map

FileDownload / File: emd_33136.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: 0.01
Minimum - Maximum-0.060514495 - 0.19226338
Average (Standard dev.)0.00047905842 (±0.004819991)
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_33136_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_33136_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 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 molecule of co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon (5'-exon)
  • Ligand: SPERMIDINE
  • 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 30nt 3'/5'-exon
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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Macromolecule #1: The Tet-S2 state molecule of co-transcriptional folded wild-type ...

MacromoleculeName: The Tet-S2 state 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: 129.222188 KDa
SequenceString: UUUGGAGGGA AAAGUUAUCA GGCAUGCACC UGGUAGCUAG UCUUUAAACC AAUAGAUUGC AUCGGUUUAA AAGGCAAGAC CGUCAAAUU GCGGGAAAGG GGUCAACAGC CGUUCAGUAC CAAGUCUCAG GGGAAACUUU GAGAUGGCCU UGCAAAGGGU A UGGUAAUA ...String:
UUUGGAGGGA AAAGUUAUCA GGCAUGCACC UGGUAGCUAG UCUUUAAACC AAUAGAUUGC AUCGGUUUAA AAGGCAAGAC CGUCAAAUU GCGGGAAAGG GGUCAACAGC CGUUCAGUAC CAAGUCUCAG GGGAAACUUU GAGAUGGCCU UGCAAAGGGU A UGGUAAUA AGCUGACGGA CAUGGUCCUA ACCACGCAGC CAAGUCCUAA GUCAACAGAU CUUCUGUUGA UAUGGAUGCA GU UCACAGA CUAAAUGUCG GUCGGGGAAG AUGUAUUCUU CUCAUAAGAU AUAGUCGGAC CUCUCCUUAA UGGGAGCUAG CGG AUGAAG UGAUGCAACA CUGGAGCCGC UGGGAACUAA UUUGUAUGCG AAAGUAUAUU GAUUAGUUUU GGAGUACUCG UAAG

GENBANK: GENBANK: X54512.1

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Macromolecule #2: The Tet-S2 state molecule of co-transcriptional folded wild-type ...

MacromoleculeName: The Tet-S2 state 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: 1.789085 KDa
SequenceString:
CUCUCU

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Macromolecule #3: SPERMIDINE

MacromoleculeName: SPERMIDINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: SPD
Molecular weightTheoretical: 145.246 Da
Chemical component information

ChemComp-SPD:
SPERMIDINE

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 29 / 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: 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
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: 1-15 / Average electron dose: 32.0 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: 3.7 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: 4188150
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7ez0

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: 1088579
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 / 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
Output model

PDB-7xd5:
The Tet-S2 state of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon

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