[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleCryo-EM structure of a natural RNA nanocage.
Journal, issue, pagesNature, Year 2025
Publish dateJun 16, 2025
AuthorsXiaobin Ling / Dmitrij Golovenko / Jianhua Gan / Jinbiao Ma / Andrei A Korostelev / Wenwen Fang /
PubMed AbstractLong (>200 nucleotides) non-coding RNAs (lncRNAs) play important roles in diverse aspects of life. Over 20 classes of lncRNAs have been identified in bacteria and bacteriophages through comparative ...Long (>200 nucleotides) non-coding RNAs (lncRNAs) play important roles in diverse aspects of life. Over 20 classes of lncRNAs have been identified in bacteria and bacteriophages through comparative genomics analyses, but their biological functions remain largely unexplored. Due to the large sizes, the structural determinants of most lncRNAs also remain uncharacterized. Here we report the structures of two natural RNA nanocages formed by the lncRNA ROOL (rumen-originating, ornate, large) found in bacterial and phage genomes. ~2.9 Å cryo-electron microscopy (cryo-EM) structures reveal that ROOL RNAs form an octameric nanocage with a 28-nm diameter and 20-nm axial length, whose hollow inside features poorly ordered regions. The octamer is stabilized by numerous tertiary and quaternary interactions, including triple-strand A-minors that we propose to name "A-minor staples". The structure of an isolated ROOL monomer at ~3.2-Å resolution indicates that nanocage assembly involves a strand-swapping mechanism resulting in quaternary kissing loops. Finally, we show that ROOL RNA fused to an RNA aptamer, tRNA, or microRNA retains its structure forming a nanocage with radially displayed cargos. Our findings therefore may enable the engineering of novel RNA nanocages as delivery vehicles for research and therapeutic applications.
External linksNature / PubMed:40523399
MethodsEM (single particle)
Resolution2.93 - 3.59 Å
Structure data

48386

9mm6

EMDB-48386, PDB-9mm6:
ROOLefa-octamer-wild type
Method: EM (single particle) / Resolution: 2.94 Å

48389

9mme

EMDB-48389, PDB-9mme:
ROOLfirm-octamer-wild type
Method: EM (single particle) / Resolution: 2.93 Å

48391

9mmg

EMDB-48391, PDB-9mmg:
ROOLefa-monomer-alone
Method: EM (single particle) / Resolution: 3.25 Å

EMDB-49873: ROOLfirm-tetramer
Method: EM (single particle) / Resolution: 3.59 Å

Chemicals

ChemComp-K:
Unknown entry

ChemComp-MG:
Unknown entry

Source
  • enterococcus faecalis jh1 (bacteria)
  • firmicutes bacterium cag:227 (bacteria)
KeywordsRNA / natural RNA nanocage / drug delivery / cryo-EM

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more