9J3R | pdb_00009j3r

Enterococcus faecalis ROOL RNA tetramer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.72 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

Cryo-EM reveals mechanisms of natural RNA multivalency.

Wang, L.Xie, J.Gong, T.Wu, H.Tu, Y.Peng, X.Shang, S.Jia, X.Ma, H.Zou, J.Xu, S.Zheng, X.Zhang, D.Liu, Y.Zhang, C.Luo, Y.Huang, Z.Shao, B.Ying, B.Cheng, Y.Guo, Y.Lai, Y.Huang, D.Liu, J.Wei, Y.Sun, S.Zhou, X.Su, Z.

(2025) Science : eadv3451-eadv3451

  • DOI: https://doi.org/10.1126/science.adv3451
  • Primary Citation of Related Structures:  
    9ISV, 9J3R, 9J3T, 9J6Y, 9KPH, 9KPO, 9L0R, 9LCR, 9LMF

  • PubMed Abstract: 

    Homo-oligomerization of biological macromolecules leads to functional assemblies that are critical to understanding various cellular processes. However, RNA quaternary structures have been rarely reported. Comparative genomics analysis has identified RNA families containing hundreds of sequences that adopt conserved secondary structures and likely fold into complex three-dimensional (3D) structures. We use 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 Å 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.


  • Organizational Affiliation

    The State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital; The State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, National Center for Stomatology, West China Hospital of Stomatology, Sichuan University, Chengdu, China.


Macromolecules
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains LengthOrganismImage
RNA (580-MER)A [auth B],
B [auth A],
C [auth D],
D [auth C]
580Enterococcus faecalis JH1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2022YFC2303700

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-19
    Type: Initial release
  • Version 1.1: 2025-03-26
    Changes: Data collection, Database references