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- EMDB-49289: A 3D density map of a 2D lattice formed by octahedral DNA origami... -

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Basic information

Entry
Database: EMDB / ID: EMD-49289
TitleA 3D density map of a 2D lattice formed by octahedral DNA origami without ferritin, was revealed by IMOD (Tomo #4).
Map data
Sample
  • Complex: 2D lattice of octahedral DNA origami without ferritin
KeywordsNon-averaged structure / individual particle cryo-electron tomography / IPET / cryo-ET / structural flexibility / DNA origami / 2D lattice / DNA-protein lattice. / DNA
Biological speciessynthetic construct (others)
Methodelectron tomography / cryo EM
AuthorsLiu J / Ren G
Funding support United States, 5 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL115153 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM104427 United States
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)R01MH077303 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK042667 United States
CitationJournal: To Be Published
Title: Non-averaged 3D structure of low-ordered 2D lattice revealed by individual-particle cryo-electron tomography
Authors: Liu J / Zhang M / Wang S / Hu Z / Wu H / Gang O / Ren G
History
DepositionFeb 18, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49289.png

Downloads & links

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Map

FileDownload / File: emd_49289.map.gz / Format: CCP4 / Size: 210.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.68 Å/pix.
x 150 pix.
= 1752. Å		11.68 Å/pix.
x 720 pix.
= 8409.601 Å		11.68 Å/pix.
x 511 pix.
= 5968.48 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 11.68 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-52931.529999999998836 - 76636.669999999998254
Average (Standard dev.)-183.061769999999996 (±8046.203000000000429)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-75
Dimensions720511150
Spacing511720150
CellA: 5968.48 Å / B: 8409.601 Å / C: 1752.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : 2D lattice of octahedral DNA origami without ferritin

EntireName: 2D lattice of octahedral DNA origami without ferritin
Components
  • Complex: 2D lattice of octahedral DNA origami without ferritin

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Supramolecule #1: 2D lattice of octahedral DNA origami without ferritin

SupramoleculeName: 2D lattice of octahedral DNA origami without ferritin / type: complex / ID: 1 / Parent: 0
Details: The octahedral DNA origami was folded by mixing 20 nM of M13mp18 scaffold DNA and 100 nM of each staple oligonucleotide in TAE buffer containing 12.5 mM MgCl2. The mixed solution was slowly ...Details: The octahedral DNA origami was folded by mixing 20 nM of M13mp18 scaffold DNA and 100 nM of each staple oligonucleotide in TAE buffer containing 12.5 mM MgCl2. The mixed solution was slowly cooled down and purified. The octahedral DNA origami was mixed in TAE/MgCl2 buffer, then the mixed solution was slowly cooled to room temperature.
Source (natural)Organism: synthetic construct (others)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation state2D array

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Sample preparation

BufferpH: 8.6
Component:
ConcentrationNameFormula
40.0 mMTris
20.0 mMAcetate
1.0 mMEDTA
12.5 mMMagnesium dichlorideMgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP
DetailsThe octahedral DNA origami was folded by mixing 20 nM of M13mp18 scaffold DNA and 100 nM of each staple oligonucleotide in TAE buffer containing 12.5 mM MgCl2. The mixed solution was slowly cooled down and purified. The octahedral DNA origami was mixed in TAE/MgCl2 buffer, then the mixed solution was slowly cooled to room temperature.
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeTFS KRIOS
TemperatureMin: 79.0 K / Max: 80.0 K
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 37 / Average exposure time: 1.0 sec. / Average electron dose: 6.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 53000
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

DetailsMotion correction of the multi-frame movie was conducted using MotionCor2. The tilt series of whole micrographs were initially aligned with IMOD.
Final reconstructionSoftware - Name: IPET / Number images used: 37
CTF correctionSoftware: (Name: Gctf, TOMOCTF)
Details: The Contrast Transfer Function (CTF) was determined by Gctf and then corrected by TOMOCTF.
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION

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