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- EMDB-51932: Small circular RNA dimer - Class 4 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51932
TitleSmall circular RNA dimer - Class 4
Map dataUnsharpened map
Sample
  • Complex: Dimer intermediate class 2 composed of 2 circular RNA and 2 complimentary RNA
    • RNA: Complementary strand
    • RNA: Circular RNA
Keywordssmall RNA circles / dimer / RNA crossover / RNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.3 Å
AuthorsMcRae EK / Kristoffersen EL / Holliger P / Andersen ES
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF21OC0070452 Denmark
CitationJournal: To Be Published
Title: Roles of dimeric intermediates in RNA-catalyzed rolling circle synthesis
Authors: Kristoffersen EL / McRae EK / Sorensen NR / Holliger P / Andersen ES
History
DepositionOct 28, 2024-
Header (metadata) releaseDec 4, 2024-
Map releaseDec 4, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51932.png

Downloads & links

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Map

FileDownload / File: emd_51932.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.59 Å/pix.
x 256 pix.
= 663.04 Å		2.59 Å/pix.
x 256 pix.
= 663.04 Å		2.59 Å/pix.
x 256 pix.
= 663.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.59 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.43
Minimum - Maximum-0.24462762 - 1.3257067
Average (Standard dev.)-0.00070819 (±0.017024633)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 663.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51932_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51932_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51932_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimer intermediate class 2 composed of 2 circular RNA and 2 compl...

EntireName: Dimer intermediate class 2 composed of 2 circular RNA and 2 complimentary RNA
Components
  • Complex: Dimer intermediate class 2 composed of 2 circular RNA and 2 complimentary RNA
    • RNA: Complementary strand
    • RNA: Circular RNA

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Supramolecule #1: Dimer intermediate class 2 composed of 2 circular RNA and 2 compl...

SupramoleculeName: Dimer intermediate class 2 composed of 2 circular RNA and 2 complimentary RNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Dimer prepared by annealing
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Complementary strand

MacromoleculeName: Complementary strand / type: rna / ID: 1 / Number of copies: 4
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.817235 KDa
SequenceString:
UGGAAGAAAU CGAAGAAGAU GAAGAACGCG AAGAAC

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Macromolecule #2: Circular RNA

MacromoleculeName: Circular RNA / type: rna / ID: 2 / Details: Circular RNA / Number of copies: 4
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.191466 KDa
SequenceString:
AUCUUCUUCG AUUUCUUCCA GUUCUUCGCG UUCUUC

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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

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 283 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 6820 / Average exposure time: 1.5 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 668921
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Software - details: NU-refinement / Number images used: 26859
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 5 / Avg.num./class: 30000 / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 231
Output model

PDB-9h86:
Small circular RNA dimer - Class 4

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