[English] 日本語
Yorodumi- EMDB-24283: Exon-free state of the Tetrahymena group I intron, symmetry-expan... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24283 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Exon-free state of the Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct | ||||||||||||||||||
Map data | Exon-free state of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct | ||||||||||||||||||
Sample |
| ||||||||||||||||||
Keywords | Ribozyme / catalytic RNA / RNA | ||||||||||||||||||
Biological species | Tetrahymena thermophila (eukaryote) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||||||||||||||
Authors | Thelot F / Liu D | ||||||||||||||||||
Funding support | United States, 5 items
| ||||||||||||||||||
Citation | Journal: Nat Methods / Year: 2022 Title: Sub-3-Å cryo-EM structure of RNA enabled by engineered homomeric self-assembly. Authors: Di Liu / François A Thélot / Joseph A Piccirilli / Maofu Liao / Peng Yin / Abstract: High-resolution structural studies are essential for understanding the folding and function of diverse RNAs. Herein, we present a nanoarchitectural engineering strategy for efficient structural ...High-resolution structural studies are essential for understanding the folding and function of diverse RNAs. Herein, we present a nanoarchitectural engineering strategy for efficient structural determination of RNA-only structures using single-particle cryogenic electron microscopy (cryo-EM). This strategy-ROCK (RNA oligomerization-enabled cryo-EM via installing kissing loops)-involves installing kissing-loop sequences onto the functionally nonessential stems of RNAs for homomeric self-assembly into closed rings with multiplied molecular weights and mitigated structural flexibility. ROCK enables cryo-EM reconstruction of the Tetrahymena group I intron at 2.98-Å resolution overall (2.85 Å for the core), allowing de novo model building of the complete RNA, including the previously unknown peripheral domains. ROCK is further applied to two smaller RNAs-the Azoarcus group I intron and the FMN riboswitch, revealing the conformational change of the former and the bound ligand in the latter. ROCK holds promise to greatly facilitate the use of cryo-EM in RNA structural studies. | ||||||||||||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_24283.map.gz | 2.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-24283-v30.xml emd-24283.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
Images | emd_24283.png | 98.9 KB | ||
Filedesc metadata | emd-24283.cif.gz | 4.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24283 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24283 | HTTPS FTP |
-Validation report
Summary document | emd_24283_validation.pdf.gz | 456.8 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_24283_full_validation.pdf.gz | 456.4 KB | Display | |
Data in XML | emd_24283_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | emd_24283_validation.cif.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24283 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24283 | HTTPS FTP |
-Related structure data
Related structure data | 7r6nMC 7r6lC 7r6mC M: atomic model generated by this map C: citing same article (ref.) |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_24283.map.gz / Format: CCP4 / Size: 2.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Exon-free state of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.24 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Sample components
-Entire : Exon-free state of Tetrahymena group I intron, symmetry-expanded ...
Entire | Name: Exon-free state of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct |
---|---|
Components |
|
-Supramolecule #1: Exon-free state of Tetrahymena group I intron, symmetry-expanded ...
Supramolecule | Name: Exon-free state of Tetrahymena group I intron, symmetry-expanded monomer from a synthetic trimeric construct type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Tetrahymena thermophila (eukaryote) / Synthetically produced: Yes |
Molecular weight | Theoretical: 130 KDa |
-Macromolecule #1: Group I intron
Macromolecule | Name: Group I intron / type: rna / ID: 1 / Number of copies: 1 |
---|---|
Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
Molecular weight | Theoretical: 127.005961 KDa |
Sequence | String: UGGAGGGAAA AGUUAUCAGG CAUGCACCUG GUAGCUAGUC UUUAAACCAA UAGAUUGCAU CGGUUUAAAA GGCAAGACCG UCAAAUUGC GGGAAAGGGG UCAACAGCCG UUCAGUACCA AGUCUCAGGG GAAACUUUGA GAUGGCCUUG CAAAGGGUAU G GUAAUAAG ...String: UGGAGGGAAA AGUUAUCAGG CAUGCACCUG GUAGCUAGUC UUUAAACCAA UAGAUUGCAU CGGUUUAAAA GGCAAGACCG UCAAAUUGC GGGAAAGGGG UCAACAGCCG UUCAGUACCA AGUCUCAGGG GAAACUUUGA GAUGGCCUUG CAAAGGGUAU G GUAAUAAG CUGACGGACA UGGUCCUAAC CACGCAGCCA AGUCCUAAGU CAACAGGAUG GUUCUGUUGA UAUGGAUGCA GU UCACAGA CUAAAUGUCG GUCGGGGAAG AUGUAUUCUU CUCAUAAGAU AUAGUCGGAC CUCUCCUUAA UGGGAGCUAG CGG AUGAAG UGAUGCAACA CUGGAGCCGC UGGGAACUAA UCAGUGAACC AUCCACUGAU UAGUUUUGGA GUACUCG GENBANK: GENBANK: V01416.1 |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 12 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| |||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / 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: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85596 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |