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- EMDB-41354: Cryo-EM structure of RNA device 43 truncation mutant 3 (U100C), a... -

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Basic information

Entry
Database: EMDB / ID: EMD-41354
TitleCryo-EM structure of RNA device 43 truncation mutant 3 (U100C), apo state
Map dataunsharpened
Sample
  • Complex: Synthetic RNA device containing hammerhead ribozyme and tetracycline-binding aptamer
    • RNA: RNA device 43 truncation mutant 3 (U100C)
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsRNA device / RNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsStagno JR / Deme JC / Lee Y-T / Wang Y-X / Lea SM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of RNA device 43 truncation mutant (U100C), apo state
Authors: Stagno JR / Deme JC / Lee Y-T / Wang Y-X / Lea SM
History
DepositionJul 25, 2023-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41354.png

Downloads & links

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Map

FileDownload / File: emd_41354.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.69 Å/pix.
x 392 pix.
= 271.656 Å		0.69 Å/pix.
x 392 pix.
= 271.656 Å		0.69 Å/pix.
x 392 pix.
= 271.656 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.693 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-0.38477743 - 1.028521
Average (Standard dev.)0.00011912428 (±0.014945127)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 271.656 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41354_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: b-factor sharpened

Fileemd_41354_additional_1.map
Annotationb-factor sharpened
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: deepEMhancer postprocessed

Fileemd_41354_additional_2.map
AnnotationdeepEMhancer postprocessed
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_41354_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_41354_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Synthetic RNA device containing hammerhead ribozyme and tetracycl...

EntireName: Synthetic RNA device containing hammerhead ribozyme and tetracycline-binding aptamer
Components
  • Complex: Synthetic RNA device containing hammerhead ribozyme and tetracycline-binding aptamer
    • RNA: RNA device 43 truncation mutant 3 (U100C)
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Synthetic RNA device containing hammerhead ribozyme and tetracycl...

SupramoleculeName: Synthetic RNA device containing hammerhead ribozyme and tetracycline-binding aptamer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 35.086 KDa

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Macromolecule #1: RNA device 43 truncation mutant 3 (U100C)

MacromoleculeName: RNA device 43 truncation mutant 3 (U100C) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 34.516688 KDa
SequenceString:
CAGGUACAUC CAGCUGAUGA GUCCCAAAUA GGACAAAAAG GGAGAGGUGA AGAAUACGAC CACCUAGGCU CGAAAGAGCC UAAAACAUA CCCUUCCUGG AUUCCUGC

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Macromolecule #2: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 10 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration1.2 mg/mL
BufferpH: 6.8
Component:
ConcentrationName
10.0 mMBis-Tris
100.0 mMpotassium chloride
1.0 mMmagnesium chloride
GridModel: Quantifoil / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Details: 30s at 30mA on each side
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 284 K / Instrument: FEI VITROBOT MARK IV
Detailsin vitro transcribed RNA

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 54.5 e/Å2
Electron beamAcceleration voltage: 300 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 404781
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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