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- EMDB-51309: DNA origami clamp positioner with attachment helices for interloc... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-51309
TitleDNA origami clamp positioner with attachment helices for interlocking into a larger multimeric DNA origami complex
Map dataMain refined map using Cryosparc C1 symmetry homogenous refinement.
Sample
  • Complex: DNA Origami
KeywordsDNA Origami / Honeycomb Lattice / V-shaped Clamp / DNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.13 Å
AuthorsAquilina M / Wilkens GD / Singleton M / Biela A / Abendstein L / Oton J / Sharp TH / Mey ASJS / Heddle JG / Dunn KE
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N013166/1 United Kingdom
CitationJournal: To Be Published
Title: DNA Origami Affinity Zones: A Customisable Testbed for Multivalent Interactions
Authors: Aquilina M / Wilkens GD / Singleton M / Biela A / Abendstein L / Oton J / Sharp TH / Mey ASJS / Heddle JG / Dunn KE
History
DepositionAug 8, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51309.png

Downloads & links

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Map

FileDownload / File: emd_51309.map.gz / Format: CCP4 / Size: 775.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain refined map using Cryosparc C1 symmetry homogenous refinement.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.7 Å/pix.
x 588 pix.
= 999.6 Å		1.7 Å/pix.
x 588 pix.
= 999.6 Å		1.7 Å/pix.
x 588 pix.
= 999.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.124
Minimum - Maximum-0.1741665 - 0.43513262
Average (Standard dev.)0.0006849756 (±0.028299142)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions588588588
Spacing588588588
CellA=B=C: 999.60004 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Map A.

Fileemd_51309_half_map_1.map
AnnotationMap A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Map B.

Fileemd_51309_half_map_2.map
AnnotationMap B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DNA Origami

EntireName: DNA Origami
Components
  • Complex: DNA Origami

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Supramolecule #1: DNA Origami

SupramoleculeName: DNA Origami / type: complex / ID: 1 / Parent: 0 / Details: Folded from a P8064 viral scaffold.
Source (natural)Organism: synthetic construct (others)

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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 / Details: 1xTE + 12.5mM MgCl2 + 5mM KCl
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV
Details: Drain time of 0s, blot force of -1, no wait time, and a blot time of 3s or 7s..
DetailsDNA origami in 1xTE + Magnesium/Potassium buffer

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 4510 / Average electron dose: 20.11 e/Å2 / Details: Movie mode, 40 frames per image.
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: 2.1 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3598 / Details: All manually selected.
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 3303
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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