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- EMDB-70036: 5mC-6HBC-Type-1-dimer RNA -

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Basic information

Entry
Database: EMDB / ID: EMD-70036
Title5mC-6HBC-Type-1-dimer RNA
Map data
Sample
  • Complex: Dimeric structure of a 6-helix bundle with a clasp helix transcribed with 5-methyl-cytidine.
    • RNA: 5mC-6HBC-type-1-dimer
KeywordsRNA / origami / 5mC / 5-methyl-cytidine / modified base
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.1 Å
AuthorsMcRae EKS / Kumar DY
Funding support United States, 1 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR230015 United States
CitationJournal: Res Sq / Year: 2025
Title: Base modifications reshape RNA folding landscapes and structure-function relationships in synthetic and natural RNAs.
Authors: Ewan McRae / Deepak Yadav / Haoyun Yang / Sukyeong Lee /
Abstract: Modified bases such as 5-methylcytosine (5mC) and N1-methyl-pseudouridine (N1Ψ) are widely used to reduce the immunogenicity of and enhance the stability and translational efficiency of therapeutic ...Modified bases such as 5-methylcytosine (5mC) and N1-methyl-pseudouridine (N1Ψ) are widely used to reduce the immunogenicity of and enhance the stability and translational efficiency of therapeutic RNAs, yet their effects on RNA 3D structure remain poorly understood. Here, we investigate how these base modifications influence the folding and function of structured RNAs using both an engineered RNA origami nanostructure and a naturally occurring ribozyme. We show that modified bases impair kinetic maturation of RNA nanostructures and promote alternative folding topologies via stabilization of noncanonical stacking arrangements. Cryo-EM and FRET experiments reveal that this conformational shift is driven not by changes in base pairing, but by altered stacking energetics at key junctions. Our findings highlight the need to consider structural consequences when using base modifications and offer design principles for the development of functional, structured RNAs in synthetic biology and therapeutic applications.
History
DepositionApr 4, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70036.png

Downloads & links

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Map

FileDownload / File: emd_70036.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 3.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0
Minimum - Maximum-0.45702288 - 2.8445363
Average (Standard dev.)-0.001609626 (±0.096022315)
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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Mask #1

Fileemd_70036_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_70036_half_map_1.map
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Half map: #2

Fileemd_70036_half_map_2.map
Projections & Slices
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Sample components

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Entire : Dimeric structure of a 6-helix bundle with a clasp helix transcri...

EntireName: Dimeric structure of a 6-helix bundle with a clasp helix transcribed with 5-methyl-cytidine.
Components
  • Complex: Dimeric structure of a 6-helix bundle with a clasp helix transcribed with 5-methyl-cytidine.
    • RNA: 5mC-6HBC-type-1-dimer

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Supramolecule #1: Dimeric structure of a 6-helix bundle with a clasp helix transcri...

SupramoleculeName: Dimeric structure of a 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: 5mC-6HBC-type-1-dimer

MacromoleculeName: 5mC-6HBC-type-1-dimer / type: rna / ID: 1 / Details: Homo-dimer
Source (natural)Organism: synthetic construct (others)
SequenceString: GGGAGAGUAC UAUUCAGAUG CAGACCGCAA GUUCAGAGCG GUUUGCAUCU AGGGUACGUU UUCGAACGUA UCCUCCGACU AAGUGUAUUC GUAUACUUAG UGCCUUGUGC CUGCUUCGGC AGGCAUGACC CAAAUGUGCC UUUCGGGGCA CAUUUCCGGU CAUCCAAGUU ...String:
GGGAGAGUAC UAUUCAGAUG CAGACCGCAA GUUCAGAGCG GUUUGCAUCU AGGGUACGUU UUCGAACGUA UCCUCCGACU AAGUGUAUUC GUAUACUUAG UGCCUUGUGC CUGCUUCGGC AGGCAUGACC CAAAUGUGCC UUUCGGGGCA CAUUUCCGGU CAUCCAAGUU CGCUUGGGUG AUGCGGGCGU AUAGGUUCGU CUAUACGUCC GCGUUUUCCG AGAAGAGGUA ACUCGGGAAA CCGGUCCACG UGACAAAGGU AGAGUUACGU GGAGGGAGCA GCUGCAAAGG GAUAAUGCAG UUGCUGGCUG GAUGCCAGAA CUCACGACUG GCAUCUACGG GGAUGGUGCU CUCCCAAUUC UCCAUUUACC GCCGAAUCGA CCCCAACGUG AGAGGGGUCG GUUCCCCGAG CAUAGACCAA UAUCCCAGGU UUAUGCUCCC CAACGCUGGA CGAACUACCU ACGUCUAGCG UUCCGGCAAA UGAGUCAAUA CCUCAGACUU AUUUGCGGUG CCUGAGCCUA AACUGAACAU GGGUUCAGGC AUCUUGGCUC CAGUUCGCUG GAGCCGACGG UAGCGCUGCG UUCGCGCAGU GCUAGGGAGC AUCCGUUUUC GAGCGGAUGC UGGGCGGUUG CCUGUUCGCA GGCAAUCGGG CCUACUCAUG AUUCGUCAUG AGUGGUGACA GCGUGAUGUU CGCAUUACGC UGUCGGGUAG AUGGAGAAUU

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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 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 15.0 kPa / Details: 15mA in gloQube
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: 17826 / Details: Blob picking on denoised micrographs
CTF correctionSoftware - Name: cryoSPARC / Details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 12.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: non-uniform refinement / Number images used: 2616
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Avg.num./class: 7000 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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