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- EMDB-74032: 5-methyl-cytidine twist corrected RNA origami 6-helix bundle type... -

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Basic information

Entry
Database: EMDB / ID: EMD-74032
Title5-methyl-cytidine twist corrected RNA origami 6-helix bundle type-2 dimer
Map dataFull map
Sample
  • Complex: Dimeric twist-corrected 6-helix bundle with a clasp helix transcribed with 5-methyl-cytidine.
    • RNA: 5-methyl-cytidine twist corrected RNA origami 6-helix bundle
KeywordsRNA / 5-methyl-cytidine / dimer
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsMcRae EKS / Yadav DK
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_74032.png

Downloads & links

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Map

FileDownload / File: emd_74032.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: 0.7
Minimum - Maximum-1.1651666 - 5.825442
Average (Standard dev.)0.0010105824 (±0.1789805)
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_74032_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_74032_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 5-methyl-cytidine.
Components
  • Complex: Dimeric twist-corrected 6-helix bundle with a clasp helix transcribed with 5-methyl-cytidine.
    • RNA: 5-methyl-cytidine 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 5-methyl-cytidine.
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: 5-methyl-cytidine twist corrected RNA origami 6-helix bundle

MacromoleculeName: 5-methyl-cytidine twist corrected RNA origami 6-helix bundle
type: rna / ID: 1 / Number of copies: 2
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 237.851219 KDa
SequenceString: GGGU(5MC)(5MC)G(5MC)A(5MC) UUUG(5MC)A(5MC)(5MC)GA G(5MC)U(5MC)U(5MC)GG(5MC)A A(5MC) AAG(5MC)(5MC)AG (5MC)(5MC)GAGAGUU(5MC) GGUAGUGGGU AUGUU(5MC)G(5MC)AU A(5MC)(5MC) (5MC)G(5MC)UU(5MC) (5MC) ...String:
GGGU(5MC)(5MC)G(5MC)A(5MC) UUUG(5MC)A(5MC)(5MC)GA G(5MC)U(5MC)U(5MC)GG(5MC)A A(5MC) AAG(5MC)(5MC)AG (5MC)(5MC)GAGAGUU(5MC) GGUAGUGGGU AUGUU(5MC)G(5MC)AU A(5MC)(5MC) (5MC)G(5MC)UU(5MC) (5MC)AGUA(5MC)G(5MC)UA AUU(5MC)GUUAGU GUA(5MC)U(5MC)(5MC)G(5MC)U GUUAAGGGU U(5MC)G(5MC)(5MC)(5MC)UUGA (5MC)AGG(5MC)(5MC)(5MC)UGA UAGU(5MC)GUU(5MC)G (5MC)GG(5MC)UAU(5MC)A G(5MC)(5MC)GGAGUGU GA(5MC)UUU(5MC)GAG UUG(5MC)A(5MC)U(5MC)GG G (5MC)(5MC)UG(5MC)AGU AUUU(5MC)GAUA(5MC) UGUGGG(5MC)(5MC)(5MC)U GU(5MC)A(5MC)AUAA (5MC)AAGGUAU(5MC)A GUUGUGUGA(5MC) A(5MC)GGG(5MC)UGGU (5MC)G(5MC)UAAAU(5MC)G A(5MC)GA UAG(5MC)G AU(5MC)AG(5MC)GG(5MC)G UGGGU(5MC)(5MC)GUA AAAGA(5MC)(5MC)GAU A(5MC)GGAU (5MC)UA (5MC)(5MC)GGGAGUUG (5MC)GAU(5MC)AAUGA UGGAGAU(5MC)GU AG(5MC)U(5MC)GGAGU AAAGU GUGG A(5MC)(5MC)(5MC)UAAGGA UAA(5MC)U(5MC)AUA(5MC) (5MC)GUGAGGGUU G(5MC)GAA(5MC) (5MC)AU (5MC)AA(5MC)G(5MC)GA(5MC)(5MC) UU(5MC)GG(5MC)(5MC)AGG GU(5MC)GUAGGAA (5MC)GG U(5MC)UA(5MC)(5MC) UA(5MC)GAU(5MC)(5MC)U(5MC) (5MC)(5MC)GAA(5MC)UGAU U(5MC)GAA(5MC) GU(5MC) GAA(5MC)GAAU(5MC)G GUU(5MC)(5MC)(5MC)G(5MC)(5MC)A GUGUUAUGAA GAUA(5MC)(5MC)A (5MC)A UAG(5MC)A(5MC)UGGG AUGUUG(5MC)GGG UA(5MC)AAGG(5MC)UU GAGUGUU(5MC)G(5MC) AAUAU (5MC)A(5MC)G GGAGU(5MC)UUU(5MC) GAGG(5MC)U(5MC)(5MC)(5MC)G U(5MC)GGAU(5MC)UAG GU (5MC)AUU(5MC)GU GA(5MC)(5MC)UAGGUG GG(5MC)AUAU(5MC)(5MC)G (5MC)(5MC)UU(5MC)GGG(5MC) GGAUGUGGG(5MC) GUGU(5MC)UGU(5MC)(5MC) UU(5MC)GGGG(5MC)AG A(5MC)A(5MC)(5MC)GGGUG (5MC)A(5MC)G(5MC)GGUU (5MC)G(5MC)(5MC)G(5MC)GUGU A(5MC)G(5MC)(5MC)A(5MC)AUA AU(5MC) (5MC)UUU(5MC)G AGGGUUAUGU GG(5MC)UAUGAGU UGU(5MC)(5MC)UUA

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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: SEC purified in 50mM HEPES pH 8.0, 50mM KCl, 5mM MgCl2
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE
DetailsSEC purified in 50mM HEPES pH 8.0, 50mM KCl, 5mM MgCl2

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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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000

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Image processing

Particle selectionNumber selected: 73602 / Details: Blob picking on denoised micrographs
CTF correctionDetails: Patch CTF / Type: 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: 11203
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3 / Avg.num./class: 10000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9zc9


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: geometry minimization
Output model

PDB-9zca:
5-methyl-cytidine twist corrected RNA origami 6-helix bundle type-2 dimer

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