[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

TitleBase modifications shift tertiary structure and activity in synthetic RNA origami and a natural ribozyme.
Journal, issue, pagesNat Commun, Year 2026
Publish dateMay 13, 2026
AuthorsDeepak Kumar Yadav / Haoyun Yang / Sukyeong Lee / Ewan K S McRae /
PubMed AbstractModified nucleotide bases like 5-methylcytosine (m5C) and N1-methyl-pseudouridine (m1Ψ) are widely used to enhance stability and reduce immunogenicity in therapeutic RNAs, yet their impact on RNA ...Modified nucleotide bases like 5-methylcytosine (m5C) and N1-methyl-pseudouridine (m1Ψ) are widely used to enhance stability and reduce immunogenicity in therapeutic RNAs, yet their impact on RNA tertiary structure remains unclear. Here we investigate how these modifications influence folding and function in both a synthetic RNA origami nanostructure and the natural Tetrahymena ribozyme. Using cryo-EM, FRET, and biochemical assays, we find that modified bases impede proper maturation of RNA origami by stabilizing alternative coaxial stacking at key junctions, leading to dimerization. In the ribozyme, modifications shift the equilibrium between open and closed conformations, altering catalytic activity in a temperature-dependent manner. These effects arise primarily from changes in base-stacking energetics rather than base pairing. Our findings reveal that base modifications reshape RNA folding landscapes and structure-function relationships, underscoring the need to consider structural consequences when designing modified RNAs for synthetic biology and therapeutic applications.
External linksNat Commun / PubMed:42128887
MethodsEM (single particle)
Resolution4.9 - 12.2 Å
Structure data

73997

9zbq

EMDB-73997, PDB-9zbq:
1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme
Method: EM (single particle) / Resolution: 5.3 Å

73998

9zbr

EMDB-73998, PDB-9zbr:
1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme - extended conformation
Method: EM (single particle) / Resolution: 7.5 Å

74032

9zca

EMDB-74032, PDB-9zca:
5-methyl-cytidine twist corrected RNA origami 6-helix bundle type-2 dimer
Method: EM (single particle) / Resolution: 11.5 Å

74033

9zcb

EMDB-74033, PDB-9zcb:
1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle type-1 dimer
Method: EM (single particle) / Resolution: 11.5 Å

PDB-9zc6:
5-methyl-cytidine L-21 ScaI Tetrahymena Ribozyme
Method: ELECTRON MICROSCOPY / Resolution: 4.9 Å

PDB-9zc7:
5-methyl-cytidine RNA origami 6-helix bundle monomer
Method: ELECTRON MICROSCOPY / Resolution: 7.9 Å

PDB-9zc8:
5-methyl-cytidine RNA origami 6-helix bundle type-1 dimer
Method: ELECTRON MICROSCOPY / Resolution: 12.1 Å

PDB-9zc9:
5-methyl-cytidine twist corrected RNA origami 6-helix bundle monomer
Method: ELECTRON MICROSCOPY / Resolution: 8 Å

PDB-9zcc:
1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle type-2 dimer
Method: ELECTRON MICROSCOPY / Resolution: 12.2 Å

Source
  • tetrahymena thermophila (eukaryote)
  • synthetic construct (others)
KeywordsRNA / Tetrahymena ribozyme / m1Y / 1-methyl-pseudouridine / modified base / 5mC / 5-methyl-cytidine / origami / homodimer / dimer

+
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