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- EMDB-6367: Electron cryo-microscopy 3D reconstruction of an octahedral DNA/A... -

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Basic information

Entry
Database: EMDB / ID: EMD-6367
TitleElectron cryo-microscopy 3D reconstruction of an octahedral DNA/AuNP hybrid nanoparticle
Map data3D reconstruction of hybrid nanoparticle with an octahedron DNA cage encapsulating a gold nanoparticle
Sample
  • Sample: Hybrid nanoparticle of octahedral DNA cage encapsulating a gold nanoparticle
  • DNA: octahedral DNA nanocage
  • Em label: gold nanoparticle
KeywordsDNA/AuNP hybrid nanoparticle
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 24.0 Å
AuthorsYu G / Yan R / Zhang C / Mao C / Jiang W
CitationJournal: Small / Year: 2015
Title: Single-Particle Cryo-EM and 3D Reconstruction of Hybrid Nanoparticles with Electron-Dense Components.
Authors: Guimei Yu / Rui Yan / Chuan Zhang / Chengde Mao / Wen Jiang /
Abstract: Single-particle cryo-electron microscopy (cryo-EM), accompanied with 3D reconstruction, is a broadly applicable tool for the structural characterization of macromolecules and nanoparticles. Recently, ...Single-particle cryo-electron microscopy (cryo-EM), accompanied with 3D reconstruction, is a broadly applicable tool for the structural characterization of macromolecules and nanoparticles. Recently, the cryo-EM field has pushed the limits of this technique to higher resolutions and samples of smaller molecular mass, however, some samples still present hurdles to this technique. Hybrid particles with electron-dense components, which have been studied using single-particle cryo-EM yet with limited success in 3D reconstruction due to the interference caused by electron-dense elements, constitute one group of such challenging samples. To process such hybrid particles, a masking method is developed in this work to adaptively remove pixels arising from electron-dense portions in individual projection images while maintaining maximal biomass signals for subsequent 2D alignment, 3D reconstruction, and iterative refinements. As demonstrated by the success in 3D reconstruction of an octahedron DNA/gold hybrid particle, which has been previously published without a 3D reconstruction, the devised strategy that combines adaptive masking and standard single-particle 3D reconstruction approach has overcome the hurdle of electron-dense elements interference, and is generally applicable to cryo-EM structural characterization of most, if not all, hybrid nanomaterials with electron-dense components.
History
DepositionJun 25, 2015-
Header (metadata) releaseJul 22, 2015-
Map releaseJul 22, 2015-
UpdateOct 21, 2015-
Current statusOct 21, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6367.png

Downloads & links

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Map

FileDownload / File: emd_6367.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D reconstruction of hybrid nanoparticle with an octahedron DNA cage encapsulating a gold nanoparticle
Voxel sizeX=Y=Z: 4.98 Å
Density
Contour LevelBy AUTHOR: 4.5 / Movie #1: 4.5
Minimum - Maximum-15.35352325 - 217.26002502
Average (Standard dev.)1.71778035 (±15.66220474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-40-40
Dimensions808080
Spacing808080
CellA=B=C: 398.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.984.984.98
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z398.400398.400398.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-40-40-40
NC/NR/NS808080
D min/max/mean-15.354217.2601.718

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Supplemental data

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Sample components

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Entire : Hybrid nanoparticle of octahedral DNA cage encapsulating a gold n...

EntireName: Hybrid nanoparticle of octahedral DNA cage encapsulating a gold nanoparticle
Components
  • Sample: Hybrid nanoparticle of octahedral DNA cage encapsulating a gold nanoparticle
  • DNA: octahedral DNA nanocage
  • Em label: gold nanoparticle

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Supramolecule #1000: Hybrid nanoparticle of octahedral DNA cage encapsulating a gold n...

SupramoleculeName: Hybrid nanoparticle of octahedral DNA cage encapsulating a gold nanoparticle
type: sample / ID: 1000
Oligomeric state: one octahedral DNA cage encapsulating one gold nanoparticle
Number unique components: 2

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Macromolecule #1: octahedral DNA nanocage

MacromoleculeName: octahedral DNA nanocage / type: dna / ID: 1 / Classification: DNA / Structure: DOUBLE HELIX / Synthetic?: Yes
Source (natural)Organism: synthetic construct (others)

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Macromolecule #2: gold nanoparticle

MacromoleculeName: gold nanoparticle / type: em_label / ID: 2 / Number of copies: 1

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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

GridDetails: 400 mesh copper grid with perforated carbon
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal magnification: 66000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateJun 5, 2013
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Average electron dose: 20 e/Å2

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Image processing

CTF correctionDetails: each particle
Final reconstructionResolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: OTHER / Software - Name: jspr / Number images used: 300
DetailsParticles were selected using e2boxer.py in EMAN2. Contrast transfer function (CTF) estimation was performed using fitctf2.py. After preprocessing (i.e., particle picking, determination of CTF parameters, and phase correction), hybrid particles were masked using maskGold.py, resulting in two sets of particles: normalized particles (.norm, with the nongold pixels normalized to mean=0 and sigma=1) and masked particles (.masked) derived from the normalized images (.norm) with gold pixels masked. The entire data set of masked images was then halved into even and odd subsets from which initial models were derived and iterative refinements were performed independently using the random initial model method. Using the initial models as references, 2D alignment was performed using projection matching and 3D models were reconstructed using the direct Fourier inversion approach. The resolution of the reconstruction was estimated based on the 0.143 cutoff of the Fourier shell correlation between models from even and odd subsets. A final map of the hybrid particle was obtained by pooling the two half data sets and applying the refinement parameters for masked particles (.masked) to the corresponding normalized particles (.norm).
FSC plot (resolution estimation)

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