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- EMDB-33136: The Tet-S2 state of wild-type Tetrahymena group I intron with 30n... -
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Open data
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Basic information
Entry | ![]() | ||||||||||||||||||||||||
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Title | The Tet-S2 state of wild-type Tetrahymena group I intron with 30nt 3'/5'-exon | ||||||||||||||||||||||||
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![]() | Catalytic RNA / 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 | ![]() | 28.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.1 KB 21.1 KB | Display Display | ![]() |
Images | ![]() | 40.5 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 33.1 MB 33.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 695.3 KB | Display | ![]() |
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Full document | ![]() | 694.9 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7xd5MC ![]() 7xd3C ![]() 7xd4C ![]() 7xd6C ![]() 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_33136_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33136_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 molecule of co-transcriptional folded wild-type ...
Macromolecule | Name: 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 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 129.222188 KDa |
Sequence | String: 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 |
-Macromolecule #2: The Tet-S2 state molecule of co-transcriptional folded wild-type ...
Macromolecule | Name: 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 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 1.789085 KDa |
Sequence | String: CUCUCU |
-Macromolecule #3: SPERMIDINE
Macromolecule | Name: SPERMIDINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: SPD |
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Molecular weight | Theoretical: 145.246 Da |
Chemical component information | ![]() ChemComp-SPD: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 29 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-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 |