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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21836 | ||||||||||||
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Title | hc16 ligase | ||||||||||||
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![]() | ribozyme / RNA | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 11.0 Å | ||||||||||||
![]() | Kappel K / Zhang K | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures. Authors: Kalli Kappel / Kaiming Zhang / Zhaoming Su / Andrew M Watkins / Wipapat Kladwang / Shanshan Li / Grigore Pintilie / Ved V Topkar / Ramya Rangan / Ivan N Zheludev / Joseph D Yesselman / Wah Chiu / Rhiju Das / ![]() ![]() Abstract: The discovery and design of biologically important RNA molecules is outpacing three-dimensional structural characterization. Here, we demonstrate that cryo-electron microscopy can routinely resolve ...The discovery and design of biologically important RNA molecules is outpacing three-dimensional structural characterization. Here, we demonstrate that cryo-electron microscopy can routinely resolve maps of RNA-only systems and that these maps enable subnanometer-resolution coordinate estimation when complemented with multidimensional chemical mapping and Rosetta DRRAFTER computational modeling. This hybrid 'Ribosolve' pipeline detects and falsifies homologies and conformational rearrangements in 11 previously unknown 119- to 338-nucleotide protein-free RNA structures: full-length Tetrahymena ribozyme, hc16 ligase with and without substrate, full-length Vibrio cholerae and Fusobacterium nucleatum glycine riboswitch aptamers with and without glycine, Mycobacterium SAM-IV riboswitch with and without S-adenosylmethionine, and the computer-designed ATP-TTR-3 aptamer with and without AMP. Simulation benchmarks, blind challenges, compensatory mutagenesis, cross-RNA homologies and internal controls demonstrate that Ribosolve can accurately resolve the global architectures of RNA molecules but does not resolve atomic details. These tests offer guidelines for making inferences in future RNA structural studies with similarly accelerated throughput. | ||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 5.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.8 KB 11.8 KB | Display Display | ![]() |
Images | ![]() | 24.8 KB | ||
Filedesc metadata | ![]() | 4.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wloMC ![]() 6wljC ![]() 6wlkC ![]() 6wllC ![]() 6wlmC ![]() 6wlnC ![]() 6wlqC ![]() 6wlrC ![]() 6wlsC ![]() 6wltC ![]() 6wluC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : hc16 ligase
Entire | Name: hc16 ligase |
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Components |
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-Supramolecule #1: hc16 ligase
Supramolecule | Name: hc16 ligase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: RNA generated by in vitro transcription |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 110 KDa |
-Macromolecule #1: RNA (338-MER)
Macromolecule | Name: RNA (338-MER) / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 109.298711 KDa |
Sequence | String: GGUAGACUCG CAGGAAGUCU ACCGAGUAAG AGAAAGAGGA AAGACGGCCA AAUUGCGGGA AAGGGGACAA CAGCCGUUCA GUACCAAGU CUCAGGGAAA CUUCAGAUGG CCUCGCAAAG GGUAUGGUAA UAAGCUGACG GACAUGGUCC UAACCACGCA G UCAAGUCC ...String: GGUAGACUCG CAGGAAGUCU ACCGAGUAAG AGAAAGAGGA AAGACGGCCA AAUUGCGGGA AAGGGGACAA CAGCCGUUCA GUACCAAGU CUCAGGGAAA CUUCAGAUGG CCUCGCAAAG GGUAUGGUAA UAAGCUGACG GACAUGGUCC UAACCACGCA G UCAAGUCC UAAGUCAACA GCCUUGGCUG UUGAUAUGGA UGCAUUUCGA UCCAACCGAG GCUCAUUCUU GUAAUUCAUG GC CGUCGGG GAGGCACUUC GGUGCCUCUG AUAACAACUU GAAAUAAGGU UGGCUCAACG GCGCGUGACA GACAAUUCGC GCU GGAACU GCAGUCGGAC CU |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 34.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21263 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |