+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31385 | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Apo L-21 ScaI Tetrahymena ribozyme | |||||||||||||||||||||
Map data | ||||||||||||||||||||||
Sample |
| |||||||||||||||||||||
Keywords | RNA structure / Tetrahymena ribozyme / RNA | |||||||||||||||||||||
Biological species | Tetrahymena thermophila (eukaryote) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.14 Å | |||||||||||||||||||||
Authors | Su Z / Zhang K | |||||||||||||||||||||
Funding support | China, United States, 6 items
| |||||||||||||||||||||
Citation | Journal: Nature / Year: 2021 Title: Cryo-EM structures of full-length Tetrahymena ribozyme at 3.1 Å resolution. Authors: Zhaoming Su / Kaiming Zhang / Kalli Kappel / Shanshan Li / Michael Z Palo / Grigore D Pintilie / Ramya Rangan / Bingnan Luo / Yuquan Wei / Rhiju Das / Wah Chiu / Abstract: Single-particle cryogenic electron microscopy (cryo-EM) has become a standard technique for determining protein structures at atomic resolution. However, cryo-EM studies of protein-free RNA are in ...Single-particle cryogenic electron microscopy (cryo-EM) has become a standard technique for determining protein structures at atomic resolution. However, cryo-EM studies of protein-free RNA are in their early days. The Tetrahymena thermophila group I self-splicing intron was the first ribozyme to be discovered and has been a prominent model system for the study of RNA catalysis and structure-function relationships, but its full structure remains unknown. Here we report cryo-EM structures of the full-length Tetrahymena ribozyme in substrate-free and bound states at a resolution of 3.1 Å. Newly resolved peripheral regions form two coaxially stacked helices; these are interconnected by two kissing loop pseudoknots that wrap around the catalytic core and include two previously unforeseen (to our knowledge) tertiary interactions. The global architecture is nearly identical in both states; only the internal guide sequence and guanosine binding site undergo a large conformational change and a localized shift, respectively, upon binding of RNA substrates. These results provide a long-sought structural view of a paradigmatic RNA enzyme and signal a new era for the cryo-EM-based study of structure-function relationships in ribozymes. | |||||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31385.map.gz | 11.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-31385-v30.xml emd-31385.xml | 15.1 KB 15.1 KB | Display Display | EMDB header |
Images | emd_31385.png | 88.9 KB | ||
Filedesc metadata | emd-31385.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31385 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31385 | HTTPS FTP |
-Validation report
Summary document | emd_31385_validation.pdf.gz | 410.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_31385_full_validation.pdf.gz | 409.9 KB | Display | |
Data in XML | emd_31385_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_31385_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31385 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31385 | HTTPS FTP |
-Related structure data
Related structure data | 7ez0MC 7ez2C M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_31385.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 0.65 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : Apo L-21 ScaI Tetrahymena ribozyme with metal ions.
Entire | Name: Apo L-21 ScaI Tetrahymena ribozyme with metal ions. |
---|---|
Components |
|
-Supramolecule #1: Apo L-21 ScaI Tetrahymena ribozyme with metal ions.
Supramolecule | Name: Apo L-21 ScaI Tetrahymena ribozyme with metal ions. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
-Macromolecule #1: Apo L-21 ScaI Tetrahymena ribozyme
Macromolecule | Name: Apo L-21 ScaI Tetrahymena ribozyme / type: rna / ID: 1 / Number of copies: 1 |
---|---|
Source (natural) | Organism: Tetrahymena thermophila (eukaryote) |
Molecular weight | Theoretical: 125.096773 KDa |
Sequence | String: GGAGGGAAAA GUUAUCAGGC AUGCACCUGG UAGCUAGUCU UUAAACCAAU AGAUUGCAUC GGUUUAAAAG GCAAGACCGU CAAAUUGCG GGAAAGGGGU CAACAGCCGU UCAGUACCAA GUCUCAGGGG AAACUUUGAG AUGGCCUUGC AAAGGGUAUG G UAAUAAGC ...String: GGAGGGAAAA GUUAUCAGGC AUGCACCUGG UAGCUAGUCU UUAAACCAAU AGAUUGCAUC GGUUUAAAAG GCAAGACCGU CAAAUUGCG GGAAAGGGGU CAACAGCCGU UCAGUACCAA GUCUCAGGGG AAACUUUGAG AUGGCCUUGC AAAGGGUAUG G UAAUAAGC UGACGGACAU GGUCCUAACC ACGCAGCCAA GUCCUAAGUC AACAGAUCUU CUGUUGAUAU GGAUGCAGUU CA CAGACUA AAUGUCGGUC GGGGAAGAUG UAUUCUUCUC AUAAGAUAUA GUCGGACCUC UCCUUAAUGG GAGCUAGCGG AUG AAGUGA UGCAACACUG GAGCCGCUGG GAACUAAUUU GUAUGCGAAA GUAUAUUGAU UAGUUUUGGA G GENBANK: GENBANK: X54512.1 |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 27 / 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 | 3 mg/mL |
---|---|
Buffer | pH: 8.1 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.36 kPa |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Temperature | Min: 78.2 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-25 / Number real images: 7577 / Average electron dose: 75.0 e/Å2 |
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 FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 215000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |