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- EMDB-34671: The intermediate pre-Tet-S1 state of G264A mutated Tetrahymena gr... -
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Open data
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Basic information
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Title | The intermediate pre-Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside | ||||||||||||||||||||||||
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![]() | Catalytic RNA / G264A mutated Tetrahymena group I intron / RNA | ||||||||||||||||||||||||
Biological species | ![]() ![]() | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.52 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) | ![]() ![]() | 20 KB 20 KB | Display Display | ![]() |
Images | ![]() | 40.4 KB | ||
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() | 33 MB 33 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 847.3 KB | Display | ![]() |
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Full document | ![]() | 846.9 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 | ![]() 8hd7MC ![]() 7xd3C ![]() 7xd4C ![]() 7xd5C ![]() 7xd6C ![]() 7xd7C ![]() 8hd6C ![]() 8i7nC M: atomic model generated by this map C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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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_34671_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34671_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 G264A mutated Tetrahymena group I intro...
Entire | Name: Co-transcriptional folded G264A mutated Tetrahymena group I intron with 6-nt 3'/5'-exon and 2-aminopurine nucleoside |
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Components |
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-Supramolecule #1: Co-transcriptional folded G264A mutated Tetrahymena group I intro...
Supramolecule | Name: Co-transcriptional folded G264A mutated Tetrahymena group I intron with 6-nt 3'/5'-exon and 2-aminopurine nucleoside type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: The intermediate pre-Tet-S1 state molecule of co-transcriptional ...
Macromolecule | Name: The intermediate pre-Tet-S1 state molecule of co-transcriptional folded G264A mutant Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 135.155719 KDa |
Sequence | String: 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 AAACUAAAUG UCGGUCGGGG AAGAUGUAUU CUUCUCAUAA GAUAUAGUCG GAC CUCUCC UUAAUGGGAG CUAGCGGAUG AAGUGAUGCA ACACUGGAGC CGCUGGGAAC UAAUUUGUAU GCGAAAGUAU AUUG AUUAG UUUUGGAGUA CUCG GENBANK: GENBANK: JN547815.1 |
-Macromolecule #2: SPERMIDINE
Macromolecule | Name: SPERMIDINE / type: ligand / ID: 2 / Number of copies: 1 / Formula: SPD |
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Molecular weight | Theoretical: 145.246 Da |
Chemical component information | ![]() ChemComp-SPD: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 27 / 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 |
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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: 0.36 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: 1-30 / Average electron dose: 55.0 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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | ![]() PDB-8hd7: |