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- EMDB-33815: Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoi... -
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Open data
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Basic information
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Title | Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the second-step self-splicing | |||||||||
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Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Li S / Michael ZP / Zhang X / Greg P / Zhang K | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Snapshots of the second-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM. Authors: Shanshan Li / Michael Z Palo / Xiaojing Zhang / Grigore Pintilie / Kaiming Zhang / ![]() ![]() Abstract: Group I introns are catalytic RNAs that coordinate two consecutive transesterification reactions for self-splicing. To understand how the group I intron promotes catalysis and coordinates self- ...Group I introns are catalytic RNAs that coordinate two consecutive transesterification reactions for self-splicing. To understand how the group I intron promotes catalysis and coordinates self-splicing reactions, we determine the structures of L-16 Tetrahymena ribozyme in complex with a 5'-splice site analog product and a 3'-splice site analog substrate using cryo-EM. We solve six conformations from a single specimen, corresponding to different splicing intermediates after the first ester-transfer reaction. The structures reveal dynamics during self-splicing, including large conformational changes of the internal guide sequence and the J5/4 junction as well as subtle rearrangements of active-site metals and the hydrogen bond formed between the 2'-OH group of A261 and the N2 group of guanosine substrate. These results help complete a detailed structural and mechanistic view of this paradigmatic group I intron undergoing the second step of self-splicing. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 32.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.8 KB 17.8 KB | Display Display | ![]() |
Images | ![]() | 53.9 KB | ||
Others | ![]() ![]() ![]() | 33 MB 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ygcMC ![]() 7yg8C ![]() 7yg9C ![]() 7ygaC ![]() 7ygbC ![]() 7ygdC 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: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
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Density Histograms |
-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
-Entire : Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoi...
Entire | Name: Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the second-step self-splicing |
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Components |
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-Supramolecule #1: Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoi...
Supramolecule | Name: Cryo-EM structure of Tetrahymena ribozyme conformation 4 undergoing the second-step self-splicing type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 130 KDa |
-Macromolecule #1: RNA (5'-R(*UP*CP*G)-3')
Macromolecule | Name: RNA (5'-R(*UP*CP*G)-3') / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 911.596 Da |
Sequence | String: UCG |
-Macromolecule #2: RNA (5'-R(*CP*CP*CP*UP*CP*UP*UP*AP*AP*CP*C)-3')
Macromolecule | Name: RNA (5'-R(*CP*CP*CP*UP*CP*UP*UP*AP*AP*CP*C)-3') / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 3.379108 KDa |
Sequence | String: CCCUCU(SSU)AAC C |
-Macromolecule #3: RNA (393-MER)
Macromolecule | Name: RNA (393-MER) / type: rna / ID: 3 / Number of copies: 1 |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 127.011883 KDa |
Sequence | String: GGUUUGGAGG GAAAAGUUAU CAGGCAUGCA CCUGGUAGCU AGUCUUUAAA CCAAUAGAUU GCAUCGGUUU AAAAGGCAAG ACCGUCAAA UUGCGGGAAA GGGGUCAACA GCCGUUCAGU ACCAAGUCUC AGGGGAAACU UUGAGAUGGC CUUGCAAAGG G UAUGGUAA ...String: GGUUUGGAGG GAAAAGUUAU CAGGCAUGCA CCUGGUAGCU AGUCUUUAAA CCAAUAGAUU GCAUCGGUUU AAAAGGCAAG ACCGUCAAA UUGCGGGAAA GGGGUCAACA GCCGUUCAGU ACCAAGUCUC AGGGGAAACU UUGAGAUGGC CUUGCAAAGG G UAUGGUAA UAAGCUGACG GACAUGGUCC UAACCACGCA GCCAAGUCCU AAGUCAACAG AUCUUCUGUU GAUAUGGAUG CA GUUCACA GACUAAAUGU CGGUCGGGGA AGAUGUAUUC UUCUCAUAAG AUAUAGUCGG ACCUCUCCUU AAUGGGAGCU AGC GGAUGA AGUGAUGCAA CACUGGAGCC GCUGGGAACU AAUUUGUAUG CGAAAGUAUA UUGAUUAGUU UUGGAGU |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 2.6 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.8 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Particle selection | Number selected: 4255846 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.3) / Number images used: 266294 |