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Open data
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Basic information
Entry | Database: PDB / ID: 6wlo | ||||||||||||
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Title | hc16 ligase models, 11.0 Angstrom resolution | ||||||||||||
![]() | RNA (338-MER) | ||||||||||||
![]() | RNA / ribozyme | ||||||||||||
Function / homology | RNA / RNA (> 10) / RNA (> 100)![]() | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 11 Å | ||||||||||||
![]() | Kappel, K. / Zhang, K. / Su, Z. / Watkins, A.M. / Kladwang, W. / Li, S. / Pintilie, G. / Topkar, V.V. / Rangan, R. / Zheludev, I.N. ...Kappel, K. / Zhang, K. / Su, Z. / Watkins, A.M. / Kladwang, W. / Li, S. / Pintilie, G. / Topkar, V.V. / Rangan, R. / Zheludev, I.N. / Yesselman, J.D. / Chiu, W. / Das, R. | ||||||||||||
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 | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 15.9 MB | Display | ![]() |
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PDB format | ![]() | 13.7 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 21836MC ![]() 6wljC ![]() 6wlkC ![]() 6wllC ![]() 6wlmC ![]() 6wlnC ![]() 6wlqC ![]() 6wlrC ![]() 6wlsC ![]() 6wltC ![]() 6wluC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Number of models | 80 |
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Components
#1: RNA chain | Mass: 109298.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: hc16 ligase / Type: COMPLEX / Details: RNA generated by in vitro transcription / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.11 MDa / Experimental value: YES |
Source (natural) | Organism: synthetic construct (others) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 34 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING ONLY |
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3D reconstruction | Resolution: 11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21263 / Symmetry type: POINT |