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- EMDB-33137: The Tet-S2 state with a pseudoknotted 4-way junction of wild-type... -
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Open data
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Basic information
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Title | 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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![]() | RNA | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | ||||||||||||||||||||||||
![]() | Luo 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 | ![]() ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 28.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.2 KB 21.2 KB | Display Display | ![]() |
Images | ![]() | 44.9 KB | ||
Filedesc metadata | ![]() | 6.3 KB | ||
Others | ![]() ![]() | 33 MB 33 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 713.4 KB | Display | ![]() |
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Full document | ![]() | 712.9 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xd6MC ![]() 7xd3C ![]() 7xd4C ![]() 7xd5C ![]() 7xd7C ![]() 8hd6C ![]() 8hd7C ![]() 8i7nC M: atomic model generated by this map C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33137_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33137_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Co-transcriptional folded wild-type Tetrahymena group I intron wi...
Entire | Name: Co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon |
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Components |
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-Supramolecule #1: Co-transcriptional folded wild-type Tetrahymena group I intron wi...
Supramolecule | Name: Co-transcriptional folded wild-type Tetrahymena group I intron with 30nt 3'/5'-exon type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: The Tet-S2 state with a pseudoknotted 4-way junction molecule of ...
Macromolecule | Name: 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 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 140.071703 KDa |
Sequence | String: 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 GENBANK: GENBANK: X54512.1 |
-Macromolecule #2: The Tet-S2 state with a pseudoknotted 4-way junction molecule of ...
Macromolecule | Name: 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 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 8.014804 KDa |
Sequence | String: ACGGCGGGAG UAACUAUGAC UCUCU |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 28 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: SPERMIDINE
Macromolecule | Name: SPERMIDINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: SPD |
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Molecular weight | Theoretical: 145.246 Da |
Chemical component information | ![]() ChemComp-SPD: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00068 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 79.3 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 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 stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |