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- EMDB-73998: 1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme - extended ... -

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Basic information

Entry
Database: EMDB / ID: EMD-73998
Title1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme - extended conformation
Map dataUnsharpened full map
Sample
  • Complex: L21-ScaI Tetrahymena ribozyme transcribed with 1-methyl-pseudouridine
    • RNA: 1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme
KeywordsRNA / Tetrahymena ribozyme / m1Y / 1-methyl-pseudouridine / modified base
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsMcRae EKS / Yang H
Funding support United States, 1 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR230015 United States
CitationJournal: To Be Published
Title: Base modifications reshape RNA folding landscapes and structure function relationships in synthetic and natural RNAs
Authors: Kumar DY / Yang H / Lee S / McRae EKS
History
DepositionNov 21, 2025-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73998.png

Downloads & links

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Map

FileDownload / File: emd_73998.map.gz / Format: CCP4 / Size: 16.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened full map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.84 Å/pix.
x 162 pix.
= 298.08 Å		1.84 Å/pix.
x 162 pix.
= 298.08 Å		1.84 Å/pix.
x 162 pix.
= 298.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.053781256 - 0.34428602
Average (Standard dev.)0.0010709701 (±0.016212987)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions162162162
Spacing162162162
CellA=B=C: 298.08002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DeepEMhancer sharpened map

Fileemd_73998_additional_1.map
AnnotationDeepEMhancer sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_73998_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_73998_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : L21-ScaI Tetrahymena ribozyme transcribed with 1-methyl-pseudouridine

EntireName: L21-ScaI Tetrahymena ribozyme transcribed with 1-methyl-pseudouridine
Components
  • Complex: L21-ScaI Tetrahymena ribozyme transcribed with 1-methyl-pseudouridine
    • RNA: 1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme

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Supramolecule #1: L21-ScaI Tetrahymena ribozyme transcribed with 1-methyl-pseudouridine

SupramoleculeName: L21-ScaI Tetrahymena ribozyme transcribed with 1-methyl-pseudouridine
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 125 KDa

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Macromolecule #1: 1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme

MacromoleculeName: 1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 126.457586 KDa
SequenceString: GGAGGGAAAA G(B8H)(B8H)A(B8H)CAGGC A(B8H)GCACC(B8H)GG (B8H)AGC(B8H)AG(B8H)C(B8H) (B8H)(B8H)AAACCAA (B8H)AGA(B8H)(B8H)GCA(B8H) CGG(B8H)(B8H)(B8H)AAAA GGCAAGACCG (B8H) CAAA(B8H)(B8H)GC ...String:
GGAGGGAAAA G(B8H)(B8H)A(B8H)CAGGC A(B8H)GCACC(B8H)GG (B8H)AGC(B8H)AG(B8H)C(B8H) (B8H)(B8H)AAACCAA (B8H)AGA(B8H)(B8H)GCA(B8H) CGG(B8H)(B8H)(B8H)AAAA GGCAAGACCG (B8H) CAAA(B8H)(B8H)GC GGGAAAGGGG (B8H)CAACAGCCG (B8H)(B8H)CAG(B8H)ACCA AG(B8H)C(B8H)CAGGG GAAAC(B8H)(B8H)(B8H)G AGA(B8H)GGCC(B8H)(B8H) GCAAAGGG(B8H)A (B8H)GG(B8H)AA(B8H)AAG C (B8H)GACGGAC A(B8H)GG(B8H)CC(B8H)AA CCACGCAGCC AAG(B8H)CC(B8H)AAG (B8H)CAACAGA(B8H)C (B8H)(B8H)C(B8H)G(B8H)(B8H)GA (B8H)A(B8H)GGA(B8H)GCA G(B8H)(B8H)CACAGAC (B8H)AAA (B8H)G(B8H)CG G(B8H)CGGGGAAG A(B8H)G(B8H)A(B8H)(B8H)C(B8H)(B8H) C(B8H)CA(B8H)AAGA (B8H)A(B8H)AG(B8H)CGGA CC(B8H)C(B8H)CC(B8H)(B8H)A A(B8H)GGGAGC(B8H)A GCGGA(B8H)GAAG (B8H)GA(B8H)GCAAC AC(B8H)GGAGCCG C(B8H)GGGAAC(B8H)A A(B8H)(B8H)(B8H)G(B8H)A(B8H)GC G AAAG(B8H)A(B8H)A (B8H)(B8H)GA(B8H)(B8H)AG(B8H)(B8H) (B8H)(B8H)GGAG

GENBANK: GENBANK: X54512.1

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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
DetailsSample was transcribed in vitro with 1-methyl-pseudouridine triphosphate in place of UTP. Purified by size exclusion chromatography and refolded by heat denaturation and cooling to room temperature prior to the addition of 10mM 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: 599317 / 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 reconstructionResolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: non-uniform refinement / Number images used: 60417
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Avg.num./class: 250000 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7xsn


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

PDB-9zbr:
1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme - extended conformation

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