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Yorodumi- EMDB-33738: Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33738 | |||||||||
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Title | Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the first-step self-splicing | |||||||||
Map data | Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the the first-step self-splicing--- unmask | |||||||||
Sample |
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Keywords | Tetrahymena ribozyme / first step of self-splicing / conformation 2 / RNA | |||||||||
Biological species | Tetrahymena (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.18 Å | |||||||||
Authors | Zhang X / Li S / Pintilie G / Palo MZ / Zhang K / Liu L | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2023 Title: Snapshots of the first-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM. Authors: Xiaojing Zhang / Shanshan Li / Grigore Pintilie / Michael Z Palo / Kaiming Zhang / Abstract: Tetrahymena ribozyme is a group I intron, whose self-splicing is the result of two sequential ester-transfer reactions. To understand how it facilitates catalysis in the first self-splicing reaction, ...Tetrahymena ribozyme is a group I intron, whose self-splicing is the result of two sequential ester-transfer reactions. To understand how it facilitates catalysis in the first self-splicing reaction, we used cryogenic electron microscopy (cryo-EM) to resolve the structures of L-16 Tetrahymena ribozyme complexed with a 11-nucleotide 5'-splice site analog substrate. Four conformations were achieved to 4.14, 3.18, 3.09 and 2.98 Å resolutions, respectively, corresponding to different splicing intermediates during the first enzymatic reaction. Comparison of these structures reveals structural alterations, including large conformational changes in IGS/IGSext (P1-P1ext duplex) and J5/4, as well as subtle local rearrangements in the G-binding site. These structural changes are required for the enzymatic activity of the Tetrahymena ribozyme. Our study demonstrates the ability of cryo-EM to capture dynamic RNA structural changes, ushering in a new era in the analysis of RNA structure-function by cryo-EM. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33738.map.gz | 31.9 MB | EMDB map data format | |
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Header (meta data) | emd-33738-v30.xml emd-33738.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
Images | emd_33738.png | 73.6 KB | ||
Others | emd_33738_additional_1.map.gz emd_33738_half_map_1.map.gz emd_33738_half_map_2.map.gz | 32.8 MB 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33738 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33738 | HTTPS FTP |
-Validation report
Summary document | emd_33738_validation.pdf.gz | 761.7 KB | Display | EMDB validaton report |
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Full document | emd_33738_full_validation.pdf.gz | 761.2 KB | Display | |
Data in XML | emd_33738_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | emd_33738_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33738 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33738 | HTTPS FTP |
-Related structure data
Related structure data | 7ycgMC 7yc8C 7ychC 7yciC 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_33738.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the the first-step self-splicing--- unmask | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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: Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing...
File | emd_33738_additional_1.map | ||||||||||||
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Annotation | Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the the first-step self-splicing--- sharp | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing...
File | emd_33738_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the the first-step self-splicing--- half | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing...
File | emd_33738_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the the first-step self-splicing--- half | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoi...
Entire | Name: Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the first-step self-splicing |
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Components |
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-Supramolecule #1: Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoi...
Supramolecule | Name: Cryo-EM structure of Tetrahymena ribozyme conformation 2 undergoing the first-step self-splicing type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Tetrahymena (eukaryote) |
Molecular weight | Theoretical: 130 KDa |
-Macromolecule #1: RNA (5'-R(*CP*CP*CP*UP*CP*UP*AP*AP*AP*CP*C)-3')
Macromolecule | Name: RNA (5'-R(*CP*CP*CP*UP*CP*UP*AP*AP*AP*CP*C)-3') / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: Tetrahymena (eukaryote) |
Molecular weight | Theoretical: 3.386082 KDa |
Sequence | String: CCCUCUAAAC C |
-Macromolecule #2: RNA (393-MER)
Macromolecule | Name: RNA (393-MER) / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: Tetrahymena (eukaryote) |
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 #3: GUANOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GTP |
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Molecular weight | Theoretical: 523.18 Da |
Chemical component information | ChemComp-GTP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |