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- EMDB-46281: A non-averaged 3D density map of an individual particle, with a 2... -

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Basic information

Entry
Database: EMDB / ID: EMD-46281
TitleA non-averaged 3D density map of an individual particle, with a 2D lattice formed by octahedral DNA origami and ferritin, was revealed by individual particle cryo-electron tomography (Particle #212).
Map data
Sample
  • Complex: 2D lattice of octahedral DNA origami with 70% loaded 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 / Resolution: 85.0 Å
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
DepositionAug 5, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_46281.png

Downloads & links

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Map

FileDownload / File: emd_46281.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.96 Å/pix.
x 256 pix.
= 757.76 Å		2.96 Å/pix.
x 256 pix.
= 757.76 Å		2.96 Å/pix.
x 256 pix.
= 757.76 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.96 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-0.7539854 - 3.1761224
Average (Standard dev.)0.07897461 (±0.28655678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 757.76 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 with 70% loaded ferritin

EntireName: 2D lattice of octahedral DNA origami with 70% loaded ferritin
Components
  • Complex: 2D lattice of octahedral DNA origami with 70% loaded ferritin

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Supramolecule #1: 2D lattice of octahedral DNA origami with 70% loaded ferritin

SupramoleculeName: 2D lattice of octahedral DNA origami with 70% loaded ferritin
type: complex / ID: 1 / Parent: 0
Details: The octahedral DNA origami was folded by mixing 20 nM of M13mp18 scaffold DNA with 100 nM of each staple oligonucleotide in TAE buffer containing 12.5 mM MgCl2. The mixed solution was then ...Details: The octahedral DNA origami was folded by mixing 20 nM of M13mp18 scaffold DNA with 100 nM of each staple oligonucleotide in TAE buffer containing 12.5 mM MgCl2. The mixed solution was then slowly cooled down and purified. Subsequently, the octahedral DNA origami was combined with ferritin in TAE/MgCl2 buffer, and 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 with ferritin in TAE/MgCl2 buffer, then the mixed solution was slowly cooled to room temperature.
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeZEISS LIBRA120PLUS
TemperatureMin: 79.0 K / Max: 80.0 K
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number grids imaged: 1 / Number real images: 35 / Average exposure time: 1.0 sec. / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 7.0 µm / Nominal magnification: 80000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

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Image processing

DetailsThe tilt series of whole micrographs were initially aligned with IMOD. Additionally, to reduce image noise, the tilt series underwent further processing with a machine learning approach, a median filter process, and a contrast enhancement method.
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 85.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IPET
Details: The resolution was measured using FSC curves from two half-maps reconstructed with even and odd tilt angles at FSC=0.5
Number images used: 1
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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