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- EMDB-49952: Dimerized subunit pair: modular DNA origami subunit with top = 14... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-49952
TitleDimerized subunit pair: modular DNA origami subunit with top = 14 poly-T, bottom = 3 poly-T overhangs
Map dataPrimary electron density map.
Sample
  • Complex: Modular DNA origami building block for self-assembly: dimer
KeywordsDNA origami / synthetic construct / DNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 39.45 Å
AuthorsVidebaek TE / Wei W-S / Rogers WB / Fraden S
Funding support United States, 4 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-2011846 United States
National Science Foundation (NSF, United States)CMMI-2323969 United States
National Science Foundation (NSF, United States)ACI-2138259 United States
National Science Foundation (NSF, United States)ACI-2138286 United States
CitationJournal: To Be Published
Title: Economical and versatile subunit design principles for self-assembled DNA origami structures
Authors: Wei W-S / Videbaek TE / Hayakawa D / Saha R / Pomo J / Arya G / Rogers WB / Fraden S
History
DepositionApr 1, 2025-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49952.png

Downloads & links

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Map

FileDownload / File: emd_49952.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary electron density map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.64 Å/pix.
x 280 pix.
= 1577.94 Å		5.64 Å/pix.
x 280 pix.
= 1577.94 Å		5.64 Å/pix.
x 280 pix.
= 1577.94 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.6355 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.079153866 - 0.27404583
Average (Standard dev.)0.00030666587 (±0.017478121)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 1577.94 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: First half map of the structure.

Fileemd_49952_half_map_1.map
AnnotationFirst half map of the structure.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Second half map of the structure.

Fileemd_49952_half_map_2.map
AnnotationSecond half map of the structure.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Modular DNA origami building block for self-assembly: dimer

EntireName: Modular DNA origami building block for self-assembly: dimer
Components
  • Complex: Modular DNA origami building block for self-assembly: dimer

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Supramolecule #1: Modular DNA origami building block for self-assembly: dimer

SupramoleculeName: Modular DNA origami building block for self-assembly: dimer
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: synthetic construct (others) / Synthetically produced: Yes
Molecular weightTheoretical: 5 MDa

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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: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 861 / Average exposure time: 4.5 sec. / Average electron dose: 29.0 e/Å2 / Details: Camera used is the Gatan OneView Camera (4k x 4k).
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 0.8 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 6062
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 39.45 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4) / Number images used: 3343
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4)
FSC plot (resolution estimation)

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