Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures.
Journal, issue, pages	Nat Methods, Vol. 17, Issue 7, Page 699-707, Year 2020
Publish date	Jul 2, 2020
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 /
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 ...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.
External links	Nat Methods / PubMed:32616928 / PubMed Central
Methods	EM (single particle)
Resolution	4.7 - 11.0 Å
Structure data	21831 6wlj EMDB-21831: ATP-TTR-3 with AMP PDB-6wlj: ATP-TTR-3 with AMP models, 9.6 Angstrom resolution Method: EM (single particle) / Resolution: 9.6 Å 21832 6wlk EMDB-21832: Apo ATP-TTR-3 PDB-6wlk: Apo ATP-TTR-3 models, 10.0 Angstrom resolution Method: EM (single particle) / Resolution: 10.0 Å 21833 6wll EMDB-21833: Apo F. nucleatum glycine riboswitch PDB-6wll: Apo F. nucleatum glycine riboswitch models, 10.0 Angstrom resolution Method: EM (single particle) / Resolution: 10.0 Å 21834 6wlm EMDB-21834: F. nucleatum glycine riboswitch with glycine PDB-6wlm: F. nucleatum glycine riboswitch with glycine models, 7.4 Angstrom resolution Method: EM (single particle) / Resolution: 7.4 Å 21835 6wln EMDB-21835: hc16 ligase product PDB-6wln: hc16 ligase product models, 10.0 Angstrom resolution Method: EM (single particle) / Resolution: 10.0 Å 21836 6wlo EMDB-21836: hc16 ligase PDB-6wlo: hc16 ligase models, 11.0 Angstrom resolution Method: EM (single particle) / Resolution: 11.0 Å 21838 6wlq EMDB-21838: Apo SAM-IV riboswitch PDB-6wlq: Apo SAM-IV riboswitch models, 4.7 Angstrom resolution Method: EM (single particle) / Resolution: 4.7 Å 21839 6wlr EMDB-21839: SAM-IV riboswitch with SAM PDB-6wlr: SAM-IV riboswitch with SAM models, 4.8 Angstrom resolution Method: EM (single particle) / Resolution: 4.8 Å 21840 6wls EMDB-21840, PDB-6wls: Tetrahymena ribozyme models, 6.8 Angstrom resolution Method: EM (single particle) / Resolution: 6.8 Å 21841 6wlt EMDB-21841: Apo V. cholerae glycine riboswitch PDB-6wlt: Apo V. cholerae glycine riboswitch models, 4.8 Angstrom resolution Method: EM (single particle) / Resolution: 4.8 Å 21842 6wlu EMDB-21842: V. cholerae glycine riboswitch with glycine PDB-6wlu: V. cholerae glycine riboswitch with glycine models, 5.7 Angstrom resolution Method: EM (single particle) / Resolution: 5.7 Å
Source	synthetic construct (others) fusobacterium nucleatum (bacteria) mycobacterium sp. (bacteria) tetrahymena thermophila (eukaryote) vibrio cholerae (bacteria)
Keywords	RNA / aptamer / riboswitch / ribozyme