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- EMDB-11170: 126 helix bundle DNA nanostructure -

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Basic information

Entry
Database: EMDB / ID: EMD-11170
Title126 helix bundle DNA nanostructure
Map datahollow cylinder shaped 126 helix bundle DNA nanostructure
Sample
  • Complex: 126 helix bundle
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.8 Å
AuthorsKube M / Kohler F / Feigl E / Nagel-Yuksel B / Willner EM / Funke JJ / Gerling T / Stommer P / Honemann MN / Martin TG ...Kube M / Kohler F / Feigl E / Nagel-Yuksel B / Willner EM / Funke JJ / Gerling T / Stommer P / Honemann MN / Martin TG / Scheres SHW / Dietz H
Funding support Germany, European Union, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
European Research Council (ERC)European Union
CitationJournal: Nat Commun / Year: 2020
Title: Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution.
Authors: Massimo Kube / Fabian Kohler / Elija Feigl / Baki Nagel-Yüksel / Elena M Willner / Jonas J Funke / Thomas Gerling / Pierre Stömmer / Maximilian N Honemann / Thomas G Martin / Sjors H W ...Authors: Massimo Kube / Fabian Kohler / Elija Feigl / Baki Nagel-Yüksel / Elena M Willner / Jonas J Funke / Thomas Gerling / Pierre Stömmer / Maximilian N Honemann / Thomas G Martin / Sjors H W Scheres / Hendrik Dietz /
Abstract: The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is ...The methods of DNA nanotechnology enable the rational design of custom shapes that self-assemble in solution from sets of DNA molecules. DNA origami, in which a long template DNA single strand is folded by many short DNA oligonucleotides, can be employed to make objects comprising hundreds of unique DNA strands and thousands of base pairs, thus in principle providing many degrees of freedom for modelling complex objects of defined 3D shapes and sizes. Here, we address the problem of accurate structural validation of DNA objects in solution with cryo-EM based methodologies. By taking into account structural fluctuations, we can determine structures with improved detail compared to previous work. To interpret the experimental cryo-EM maps, we present molecular-dynamics-based methods for building pseudo-atomic models in a semi-automated fashion. Among other features, our data allows discerning details such as helical grooves, single-strand versus double-strand crossovers, backbone phosphate positions, and single-strand breaks. Obtaining this higher level of detail is a step forward that now allows designers to inspect and refine their designs with base-pair level interventions.
History
DepositionJun 12, 2020-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateDec 30, 2020-
Current statusDec 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11170.png

Downloads & links

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Map

FileDownload / File: emd_11170.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhollow cylinder shaped 126 helix bundle DNA nanostructure
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.78 Å/pix.
x 300 pix.
= 834. Å		2.78 Å/pix.
x 300 pix.
= 834. Å		2.78 Å/pix.
x 300 pix.
= 834. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.78 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.18451083 - 0.49427196
Average (Standard dev.)0.0013490451 (±0.02587015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 834.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.782.782.78
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z834.000834.000834.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.1850.4940.001

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Supplemental data

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Additional map: Body 4 of Multibody Refinement

Fileemd_11170_additional_1.map
AnnotationBody 4 of Multibody Refinement
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Additional map: Composite map of Multibody Refinement (Relion) with 6 bodies

Fileemd_11170_additional_2.map
AnnotationComposite map of Multibody Refinement (Relion) with 6 bodies
Projections & Slices
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Additional map: Body 3 of Multibody Refinement

Fileemd_11170_additional_3.map
AnnotationBody 3 of Multibody Refinement
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Additional map: Body 1 of Multibody Refinement

Fileemd_11170_additional_4.map
AnnotationBody 1 of Multibody Refinement
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Additional map: Body 2 of Multibody Refinement

Fileemd_11170_additional_5.map
AnnotationBody 2 of Multibody Refinement
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Body 5 of Multibody Refinement

Fileemd_11170_additional_6.map
AnnotationBody 5 of Multibody Refinement
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Body 6 of Multibody Refinement

Fileemd_11170_additional_7.map
AnnotationBody 6 of Multibody Refinement
Projections & Slices
AxesZYX

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Sample components

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Entire : 126 helix bundle

EntireName: 126 helix bundle
Components
  • Complex: 126 helix bundle

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Supramolecule #1: 126 helix bundle

SupramoleculeName: 126 helix bundle / type: complex / ID: 1 / Parent: 0
Details: hollow cylinder-shaped multilayer DNA nanostructure with 126 helices arranged on a honey comb lattice
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: 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
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
Detailsmonodisperse, 1200nM

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: CEOS Cs corrector
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number real images: 5005 / Average electron dose: 50.0 e/Å2 / Details: magnified pixel size 1.39 A
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 0.3688 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 3.6056 µm / Nominal magnification: 47000
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

CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 2), RELION (ver. 3))
Details: Resolution of bodies (1-6) from multibody refinement: 8.9, 9.7, 8.9, 8.9, 8.2, 8.2
Number images used: 122493
Initial angle assignmentType: OTHER / Software: (Name: RELION (ver. 2), RELION (ver. 3))
Details: maximum a posteriori (MAP), REgularized LIkelihood OptimizatioN (Relion)
Final angle assignmentType: OTHER / Software: (Name: RELION (ver. 2), RELION (ver. 3))
Details: maximum a posteriori (MAP), REgularized LIkelihood OptimizatioN (Relion)
FSC plot (resolution estimation)

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