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	Cryo-EM reveals mechanisms of natural RNA multivalency.
Journal, issue, pages	Science, Vol. 388, Issue 6746, Page 545-550, Year 2025
Publish date	Mar 13, 2025
Authors	Liu Wang / Jiahao Xie / Tao Gong / Hao Wu / Yifan Tu / Xin Peng / Sitong Shang / Xinyu Jia / Haiyun Ma / Jian Zou / Sheng Xu / Xin Zheng / Dong Zhang / Yang Liu / Chong Zhang / Yongbo Luo / Zirui Huang / Bin Shao / Binwu Ying / Yu Cheng / Yingqiang Guo / Ying Lai / Dingming Huang / Jianquan Liu / Yuquan Wei / Siqi Sun / Xuedong Zhou / Zhaoming Su /
PubMed Abstract	Homo-oligomerization of biological macromolecules leads to functional assemblies that are critical to understanding various cellular processes. However, RNA quaternary structures have rarely been ...Homo-oligomerization of biological macromolecules leads to functional assemblies that are critical to understanding various cellular processes. However, RNA quaternary structures have rarely been reported. Comparative genomics analysis has identified RNA families containing hundreds of sequences that adopt conserved secondary structures and likely fold into complex three-dimensional structures. In this study, we used cryo-electron microscopy (cryo-EM) to determine structures from four RNA families, including ARRPOF and OLE forming dimers and ROOL and GOLLD forming hexameric, octameric, and dodecameric nanostructures, at 2.6- to 4.6-angstrom resolutions. These homo-oligomeric assemblies reveal a plethora of structural motifs that contribute to RNA multivalency, including kissing-loop, palindromic base-pairing, A-stacking, metal ion coordination, pseudoknot, and minor-groove interactions. These results provide the molecular basis of intermolecular interactions driving RNA multivalency with potential functional relevance.
External links	Science / PubMed:40080543
Methods	EM (single particle)
Resolution	2.6 - 6.61 Å
Structure data	60850 9isv EMDB-60850, PDB-9isv: Enterococcus faecalis ROOL RNA monomer Method: EM (single particle) / Resolution: 3.07 Å 61123 9j3r EMDB-61123: Enterococcus faecalis ncRNA tetramer PDB-9j3r: Enterococcus faecalis ROOL RNA tetramer Method: EM (single particle) / Resolution: 4.72 Å 61125 9j3t EMDB-61125: Enterococcus faecalis ncRNA octamer PDB-9j3t: Enterococcus faecalis ROOL RNA octamer Method: EM (single particle) / Resolution: 3.8 Å 61189 9j6y EMDB-61189: lactobacillus salivarius ncRNA hexamer PDB-9j6y: Lactobacillus salivarius ROOL RNA hexamer Method: EM (single particle) / Resolution: 3.25 Å 62487 9kph EMDB-62487: Fusobacterium ncRNA dimer PDB-9kph: Fusobacterium nucleatum ARRPOF RNA dimer conformation 2 Method: EM (single particle) / Resolution: 3.93 Å 62489 9kpo EMDB-62489: Fusobacterium ncRNA dimer2 PDB-9kpo: Fusobacterium nucleatum ARRPOF RNA dimer conformation 1 Method: EM (single particle) / Resolution: 3.98 Å 62721 9l0r EMDB-62721: Streptococcus agalactiae ncRNA decocamer PDB-9l0r: Streptococcus agalactiae GOLLD RNA dodecamer Method: EM (single particle) / Resolution: 4.72 Å EMDB-62724: Streptococcus agalactiae GOLLD RNA 3' domain dodecamer Method: EM (single particle) / Resolution: 6.61 Å 62991 9lcr EMDB-62991: Clostridium botulinum ncRNA homo-dimer PDB-9lcr: Clostridium botulinum OLE RNA dimer Method: EM (single particle) / Resolution: 2.6 Å 63218 9lmf EMDB-63218, PDB-9lmf: Streptococcus agalactiae GOLLD RNA 3' domain decamer Method: EM (single particle) / Resolution: 3.93 Å
Chemicals	ChemComp-MG: Unknown entry
Source	enterococcus faecalis (bacteria) enterococcus faecalis jh1 (bacteria) ligilactobacillus salivarius dsm 20555 = atcc 11741 (bacteria) fusobacterium nucleatum (bacteria) streptococcus agalactiae (bacteria) clostridium botulinum a str. atcc 19397 (bacteria)
Keywords	RNA / CryoEM / ncRNA