[English] 日本語
![](img/lk-miru.gif)
- EMDB-33816: Cryo-EM structure of Tetrahymena ribozyme conformation 6 undergoi... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Tetrahymena ribozyme conformation 6 undergoing the second-step self-splicing | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Tetrahymena ribozyme / second step of self-splicing / conformation 1 / RNA | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.41 Å | |||||||||
![]() | Li S / Michael ZP / Zhang X / Greg P / Zhang K / Liu L | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 32.1 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 17.7 KB 17.7 KB | Display Display | ![]() |
Images | ![]() | 50 KB | ||
Filedesc metadata | ![]() | 5.1 KB | ||
Others | ![]() ![]() ![]() | 59.4 MB 59.4 MB 59.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 14.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ygdMC ![]() 7yg8C ![]() 7yg9C ![]() 7ygaC ![]() 7ygbC ![]() 7ygcC M: atomic model generated by this map C: citing same article ( |
---|
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: #1
File | emd_33816_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_33816_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_33816_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Cryo-EM structure of Tetrahymena ribozyme conformation 6 undergoi...
Entire | Name: Cryo-EM structure of Tetrahymena ribozyme conformation 6 undergoing the second-step self-splicing |
---|---|
Components |
|
-Supramolecule #1: Cryo-EM structure of Tetrahymena ribozyme conformation 6 undergoi...
Supramolecule | Name: Cryo-EM structure of Tetrahymena ribozyme conformation 6 undergoing the second-step self-splicing type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
---|---|
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 |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 911.596 Da |
Sequence | String: UCG |
-Macromolecule #2: RNA (5'-R(*CP*C)-3')
Macromolecule | Name: RNA (5'-R(*CP*C)-3') / type: rna / ID: 2 / Number of copies: 1 |
---|---|
Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 1.788101 KDa |
Sequence | String: CCCUCU |
-Macromolecule #3: RNA (384-MER)
Macromolecule | Name: RNA (384-MER) / type: rna / ID: 3 / Number of copies: 1 |
---|---|
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 GENBANK: GENBANK: X54512.1 |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 2.6 mg/mL |
---|---|
Buffer | pH: 8 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-
Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.8 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |