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Yorodumi- EMDB-34670: The relaxed pre-Tet-S1 state of G264A mutated Tetrahymena group I... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34670 | ||||||||||||||||||||||||
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Title | The relaxed pre-Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside | ||||||||||||||||||||||||
Map data | |||||||||||||||||||||||||
Sample |
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Biological species | Tetrahymena thermophila (eukaryote) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.73 Å | ||||||||||||||||||||||||
Authors | 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 | China, Poland, European Union, 7 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34670.map.gz | 28.6 MB | EMDB map data format | |
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Header (meta data) | emd-34670-v30.xml emd-34670.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
Images | emd_34670.png | 46.9 KB | ||
Others | emd_34670_half_map_1.map.gz emd_34670_half_map_2.map.gz | 33.1 MB 33.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34670 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34670 | HTTPS FTP |
-Related structure data
Related structure data | 8hd6MC 7xd3C 7xd4C 7xd5C 7xd6C 7xd7C 8hd7C 8i7nC M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_34670.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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_34670_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34670_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Co-transcriptional folded G264A mutant Tetrahymena group I intron...
Entire | Name: Co-transcriptional folded G264A mutant Tetrahymena group I intron with 6nt 5'/3'-exon and 2-aminopurine nucleoside |
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Components |
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-Supramolecule #1: Co-transcriptional folded G264A mutant Tetrahymena group I intron...
Supramolecule | Name: Co-transcriptional folded G264A mutant Tetrahymena group I intron with 6nt 5'/3'-exon and 2-aminopurine nucleoside type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
-Macromolecule #1: The relaxed pre-Tet-S1 state molecule of co-transcriptional folde...
Macromolecule | Name: The relaxed 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: Tetrahymena thermophila (eukaryote) |
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 |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 24 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-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: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.7 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000 |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Temperature | Min: 79.3 K |
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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 4012136 |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
Final 3D classification | Number classes: 6 / Software - Name: RELION (ver. 3.1) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 194382 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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Output model | PDB-8hd6: |