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- EMDB-74033: 1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle... -

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Basic information

Entry
Database: EMDB / ID: EMD-74033
Title1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle type-1 dimer
Map dataFull map
Sample
  • Complex: Dimeric twist-corrected 6-helix bundle with a clasp helix transcribed with 1-methyl-pseudouridine.
    • RNA: 1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle
KeywordsRNA / homodimer / 1-methyl-pseudouridine
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsMcRae EKS / Kumar YD
Funding support United States, 1 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR230015 United States
CitationJournal: Nat Commun / Year: 2026
Title: Base modifications shift tertiary structure and activity in synthetic RNA origami and a natural ribozyme.
Authors: Deepak Kumar Yadav / Haoyun Yang / Sukyeong Lee / Ewan K S McRae /
Abstract: 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 ...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.
History
DepositionNov 22, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74033.png

Downloads & links

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Map

FileDownload / File: emd_74033.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.68 Å/pix.
x 180 pix.
= 662.4 Å		3.68 Å/pix.
x 180 pix.
= 662.4 Å		3.68 Å/pix.
x 180 pix.
= 662.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.0450372 - 5.5623064
Average (Standard dev.)-0.0017656911 (±0.18142185)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 662.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_74033_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_74033_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimeric twist-corrected 6-helix bundle with a clasp helix transcr...

EntireName: Dimeric twist-corrected 6-helix bundle with a clasp helix transcribed with 1-methyl-pseudouridine.
Components
  • Complex: Dimeric twist-corrected 6-helix bundle with a clasp helix transcribed with 1-methyl-pseudouridine.
    • RNA: 1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle

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Supramolecule #1: Dimeric twist-corrected 6-helix bundle with a clasp helix transcr...

SupramoleculeName: Dimeric twist-corrected 6-helix bundle with a clasp helix transcribed with 1-methyl-pseudouridine.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 464 KDa

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Macromolecule #1: 1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle

MacromoleculeName: 1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle
type: rna / ID: 1 / Number of copies: 2
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 237.739094 KDa
SequenceString: GGG(B8H)CCGCAC (B8H)(B8H)(B8H)GCACCGA GC(B8H)C(B8H)CGGCA ACAAGCCAGC CGAGAG(B8H)(B8H) C GG(B8H)AG(B8H)GGG(B8H) A(B8H)G(B8H)(B8H)CGCA(B8H) ACCCGC(B8H)(B8H)CC AG(B8H)ACGC (B8H)A A(B8H)(B8H) ...String:
GGG(B8H)CCGCAC (B8H)(B8H)(B8H)GCACCGA GC(B8H)C(B8H)CGGCA ACAAGCCAGC CGAGAG(B8H)(B8H) C GG(B8H)AG(B8H)GGG(B8H) A(B8H)G(B8H)(B8H)CGCA(B8H) ACCCGC(B8H)(B8H)CC AG(B8H)ACGC (B8H)A A(B8H)(B8H)CG(B8H)(B8H)AG(B8H) G(B8H)AC(B8H)CCGC(B8H) G(B8H)(B8H)AAGGG(B8H) (B8H)CGCCC(B8H)(B8H)GA CAGGCCC(B8H)GA (B8H)AG(B8H)CG(B8H)(B8H)CG CGGC(B8H)A(B8H)CAG CCGGAG(B8H)G(B8H) GAC(B8H)(B8H)(B8H)CGAG (B8H)(B8H)GCAC(B8H)CGG GCC(B8H)GCAG(B8H)A (B8H)(B8H)(B8H)CGA(B8H)AC (B8H)G(B8H)GGGCCC(B8H) G(B8H)CACA(B8H)AAC AAGG(B8H)A(B8H) CA G(B8H)(B8H)G(B8H)G(B8H)GAC ACGGGC(B8H)GG(B8H) CGC(B8H)AAA(B8H)CG ACGA(B8H)AGCGA (B8H)CAGCGGCG (B8H)GGG(B8H)CCG(B8H)A AAAGACCGA(B8H) ACGGA(B8H)C(B8H)AC CGGGAG(B8H) (B8H)G CGA(B8H)CAA(B8H)GA (B8H)GGAGA(B8H)CG(B8H) AGC(B8H)CGGAG(B8H) AAAG(B8H)G(B8H)G G ACCC(B8H)AAGGA (B8H)AAC(B8H)CA(B8H)AC CG(B8H)GAGGG(B8H)(B8H) GCGAACCA(B8H)C AACGCGA CC (B8H)(B8H)CGGCCAGG G(B8H)CG(B8H)AGGAA CGG(B8H)C(B8H)ACC(B8H) ACGA(B8H)CC(B8H)CC CG AAC(B8H)GA(B8H) (B8H)CGAACG(B8H)CG AACGAA(B8H)CGG (B8H)(B8H)CCCGCCAG (B8H)G(B8H) (B8H)A(B8H)GAA GA(B8H)ACCACA(B8H) AGCAC(B8H)GGGA (B8H)G(B8H)(B8H)GCGGG(B8H) ACAAGGC (B8H)(B8H) GAG(B8H)G(B8H)(B8H)CGC AA(B8H)A(B8H)CACGG GAG(B8H)C(B8H)(B8H)(B8H)CG AGGC (B8H)CCCG (B8H)CGGA(B8H)C(B8H)AG G(B8H)CA(B8H)(B8H)CG(B8H)G ACC(B8H)AGG(B8H)GG GCA (B8H)A(B8H)CCG CC(B8H)(B8H)CGGGCG GA(B8H)G(B8H)GGGCG (B8H)G(B8H)C(B8H)G(B8H)CC(B8H) (B8H)CGGGGCAG ACACCGGG(B8H)G CACGCGG(B8H)(B8H)C GCCGCG(B8H)G(B8H)A CGCCACA(B8H)AA (B8H)CC(B8H)(B8H)(B8H)CGA GGG(B8H)(B8H)A(B8H)G(B8H)G GC(B8H)A(B8H)GAG(B8H)(B8H) G (B8H)CC(B8H)(B8H)A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 8 / Details: 50mM HEPES pH 8.0, 50mM KCl, 5mM MgCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE
DetailsIn vitro transcribed with 1-methyl-pseudouridine triphosphate in place of UTP. Purified by size exclusion chromatography.

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 11.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 8333
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT / Target criteria: geometry minimization
Output model

PDB-9zcb:
1-methyl-pseudouridine twist corrected RNA origami 6-helix bundle type-1 dimer

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