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- EMDB-67284: Octahedral Symmetry of DNA Tesseract -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-67284
TitleOctahedral Symmetry of DNA Tesseract
Map data
Sample
  • Complex: DNA tesseract nanostructure
KeywordsDNA Tesseract / DNA Nanostructure / DNA
Biological speciesNot Applicable (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 14.16 Å
AuthorsShiu SCC
Funding support Hong Kong, 3 items
OrganizationGrant numberCountry
Other government17125920 Hong Kong
Other government17125221
Other government17127124
CitationJournal: To Be Published
Title: DNA Tesseract
Authors: Shiu SCC / Deluca M / Chui WH / Zhang P / Mo X / Siu RHP / Dong E / Qu S / Cheung CCL / Kinghorn AB / Whitehouse WL / Cui J / He W / Wang XY / Li J / Khan AG / von Torklus SH / Yu TF / Al- ...Authors: Shiu SCC / Deluca M / Chui WH / Zhang P / Mo X / Siu RHP / Dong E / Qu S / Cheung CCL / Kinghorn AB / Whitehouse WL / Cui J / He W / Wang XY / Li J / Khan AG / von Torklus SH / Yu TF / Al-Jamal KT / Tse ECM / Arya G / Fang NX / Zhou K / Tanner JA
History
DepositionNov 25, 2025-
Header (metadata) releaseDec 10, 2025-
Map releaseDec 10, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67284.png

Downloads & links

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Map

FileDownload / File: emd_67284.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 400 pix.
= 382.28 Å		0.96 Å/pix.
x 400 pix.
= 382.28 Å		0.96 Å/pix.
x 400 pix.
= 382.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9557 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0445
Minimum - Maximum-0.031839613 - 0.12441342
Average (Standard dev.)0.0007036248 (±0.008328172)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 382.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : DNA tesseract nanostructure

EntireName: DNA tesseract nanostructure
Components
  • Complex: DNA tesseract nanostructure

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Supramolecule #1: DNA tesseract nanostructure

SupramoleculeName: DNA tesseract nanostructure / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Not Applicable (fungus)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 14.16 Å / Resolution method: OTHER / Software - Name: cryoSPARC / Number images used: 4745
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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