6WLO

hc16 ligase models, 11.0 Angstrom resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures.

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.

(2020) Nat Methods 17: 699-707

  • DOI: 10.1038/s41592-020-0878-9
  • Primary Citation of Related Structures:  
    6WLJ, 6WLK, 6WLL, 6WLM, 6WLN, 6WLO, 6WLQ, 6WLR, 6WLS, 6WLT, 6WLU

  • PubMed 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 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 ...

    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.


    Organizational Affiliation

    Department of Physics, Stanford University, Stanford, CA, USA. rhiju@stanford.edu.



Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsLengthOrganismImage
RNA (338-MER)A 338synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.0 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited StatesS10 OD021600
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI145647
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103832, R01GM079429, U54GM103297, R35 GM112579

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-08
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references