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Yorodumi- EMDB-24284: Azoarcus group I intron, symmetry-expanded monomer from a synthet... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24284 | ||||||||||||||||||
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Title | Azoarcus group I intron, symmetry-expanded monomer from a synthetic trimeric construct | ||||||||||||||||||
Map data | Azoarcus group I intron, symmetry-expanded monomer from a synthetic trimeric construct | ||||||||||||||||||
Sample |
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Biological species | Azoarcus olearius (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.9 Å | ||||||||||||||||||
Authors | Thelot F / Liu D / Liao M / Yin P | ||||||||||||||||||
Funding support | United States, 5 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_24284.map.gz | 5.2 MB | EMDB map data format | |
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Header (meta data) | emd-24284-v30.xml emd-24284.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_24284.png | 64.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24284 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24284 | HTTPS FTP |
-Validation report
Summary document | emd_24284_validation.pdf.gz | 326 KB | Display | EMDB validaton report |
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Full document | emd_24284_full_validation.pdf.gz | 325.5 KB | Display | |
Data in XML | emd_24284_validation.xml.gz | 4.3 KB | Display | |
Data in CIF | emd_24284_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24284 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24284 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_24284.map.gz / Format: CCP4 / Size: 5.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Azoarcus 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: 1.23 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Azoarcus group I intron, symmetry-expanded monomer from a synthet...
Entire | Name: Azoarcus group I intron, symmetry-expanded monomer from a synthetic trimeric construct |
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Components |
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-Supramolecule #1: Azoarcus group I intron, symmetry-expanded monomer from a synthet...
Supramolecule | Name: Azoarcus group I intron, symmetry-expanded monomer from a synthetic trimeric construct type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Azoarcus olearius (bacteria) |
Molecular weight | Theoretical: 80 KDa |
-Macromolecule #1: Azoarcus group I intron
Macromolecule | Name: Azoarcus group I intron / type: rna / ID: 1 |
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Source (natural) | Organism: Azoarcus olearius (bacteria) |
Sequence | String: GGCCGUGUGC CUUGCGCCGG GAAACCACGC AAGGGAUGGU GUCAAAUUCG GCGAAACCUA AGCGCGGAUG GUUCGCGUAU GGCAACGCCG AGCCAAGCUU CGCAGCCUUC GGGCUGCGAU GAAGGUGUAG AGACUAGACG GCACCCACCU AAGGCGCACC GAACCAUCCG ...String: GGCCGUGUGC CUUGCGCCGG GAAACCACGC AAGGGAUGGU GUCAAAUUCG GCGAAACCUA AGCGCGGAUG GUUCGCGUAU GGCAACGCCG AGCCAAGCUU CGCAGCCUUC GGGCUGCGAU GAAGGUGUAG AGACUAGACG GCACCCACCU AAGGCGCACC GAACCAUCCG GUGCGCUAUG GUGAAGGCAU AGUCCAGGGA GUGGCGAAAG CCACACAAAC CAG |
-Macromolecule #2: Ligated exon mimic of the Azoarcus Group I intron
Macromolecule | Name: Ligated exon mimic of the Azoarcus Group I intron / type: other / ID: 2 Classification: polydeoxyribonucleotide/polyribonucleotide hybrid |
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Source (natural) | Organism: Azoarcus olearius (bacteria) |
Sequence | String: CATACGGCC |
-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: 8 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 | |||||||||
Vitrification | Cryogen name: ETHANE / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.0 mm / Nominal magnification: 31000 |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 486860 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |