EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures.
ジャーナル・号・ページ	Nat Methods, Vol. 17, Issue 7, Page 699-707, Year 2020
掲載日	2020年7月2日
著者	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 要旨	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.
リンク	Nat Methods / PubMed:32616928 / PubMed Central
手法	EM (単粒子)
解像度	4.7 - 11.0 Å
構造データ	21831 6wlj EMDB-21831: ATP-TTR-3 with AMP PDB-6wlj: ATP-TTR-3 with AMP models, 9.6 Angstrom resolution 手法: EM (単粒子) / 解像度: 9.6 Å 21832 6wlk EMDB-21832: Apo ATP-TTR-3 PDB-6wlk: Apo ATP-TTR-3 models, 10.0 Angstrom resolution 手法: EM (単粒子) / 解像度: 10.0 Å 21833 6wll EMDB-21833: Apo F. nucleatum glycine riboswitch PDB-6wll: Apo F. nucleatum glycine riboswitch models, 10.0 Angstrom resolution 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 7.4 Å 21835 6wln EMDB-21835: hc16 ligase product PDB-6wln: hc16 ligase product models, 10.0 Angstrom resolution 手法: EM (単粒子) / 解像度: 10.0 Å 21836 6wlo EMDB-21836: hc16 ligase PDB-6wlo: hc16 ligase models, 11.0 Angstrom resolution 手法: EM (単粒子) / 解像度: 11.0 Å 21838 6wlq EMDB-21838: Apo SAM-IV riboswitch PDB-6wlq: Apo SAM-IV riboswitch models, 4.7 Angstrom resolution 手法: EM (単粒子) / 解像度: 4.7 Å 21839 6wlr EMDB-21839: SAM-IV riboswitch with SAM PDB-6wlr: SAM-IV riboswitch with SAM models, 4.8 Angstrom resolution 手法: EM (単粒子) / 解像度: 4.8 Å 21840 6wls EMDB-21840, PDB-6wls: Tetrahymena ribozyme models, 6.8 Angstrom resolution 手法: EM (単粒子) / 解像度: 6.8 Å 21841 6wlt EMDB-21841: Apo V. cholerae glycine riboswitch PDB-6wlt: Apo V. cholerae glycine riboswitch models, 4.8 Angstrom resolution 手法: EM (単粒子) / 解像度: 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 手法: EM (単粒子) / 解像度: 5.7 Å
由来	synthetic construct (人工物) fusobacterium nucleatum (バクテリア) mycobacterium sp. (マイコバクテリウム属) tetrahymena thermophila (真核生物) vibrio cholerae (コレラ菌)
キーワード	RNA (リボ核酸) / aptamer (アプタマー) / riboswitch (リボスイッチ) / ribozyme (リボザイム)