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- EMDB-11367: 16 helix bundle -

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Basic information

Entry
Database: EMDB / ID: EMD-11367
Title16 helix bundle
Map data16 helix bundle
Sample
  • Complex: 16 helix bundle
    • Complex: DNA
      • DNA: x 1 types
    • Complex: DNA Staple
      • DNA: x 36 types
Biological speciesEscherichia virus M13 / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.0 Å
AuthorsKube M / Kohler F / Feigl E
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
European Research Council (ERC) Germany
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
DepositionJul 10, 2020-
Header (metadata) releaseNov 18, 2020-
Map releaseNov 18, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.17
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.17
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7arq
  • Surface level: 0.17
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11367.png

Downloads & links

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Map

FileDownload / File: emd_11367.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation16 helix bundle
Voxel sizeX=Y=Z: 2.3 Å
Density
Contour LevelBy AUTHOR: 0.17 / Movie #1: 0.17
Minimum - Maximum-0.11610801 - 0.5509586
Average (Standard dev.)0.00004327917 (±0.015701517)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 828.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.32.32.3
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z828.000828.000828.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.1160.5510.000

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Supplemental data

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Sample components

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Entire : 16 helix bundle

EntireName: 16 helix bundle
Components
  • Complex: 16 helix bundle
    • Complex: DNA
      • DNA: DNA Staple
    • Complex: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple
      • DNA: DNA Staple

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Supramolecule #1: 16 helix bundle

SupramoleculeName: 16 helix bundle / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: DNA Origami

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Supramolecule #2: DNA

SupramoleculeName: DNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia virus M13

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Supramolecule #3: DNA Staple

SupramoleculeName: DNA Staple / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#37
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: synthetic construct (others)

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Macromolecule #1: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia virus M13
Molecular weightTheoretical: 406.694219 KDa
SequenceString: (DA)(DC)(DC)(DA)(DA)(DC)(DT)(DT)(DC)(DC) (DC)(DG)(DT)(DC)(DC)(DG)(DA)(DC)(DG)(DG) (DT)(DC)(DC)(DG)(DG)(DT)(DT)(DA)(DT) (DG)(DC)(DA)(DG)(DA)(DA)(DA)(DA)(DA)(DA) (DA) (DC)(DC)(DA)(DT)(DG)(DG) ...String:
(DA)(DC)(DC)(DA)(DA)(DC)(DT)(DT)(DC)(DC) (DC)(DG)(DT)(DC)(DC)(DG)(DA)(DC)(DG)(DG) (DT)(DC)(DC)(DG)(DG)(DT)(DT)(DA)(DT) (DG)(DC)(DA)(DG)(DA)(DA)(DA)(DA)(DA)(DA) (DA) (DC)(DC)(DA)(DT)(DG)(DG)(DG)(DT) (DT)(DG)(DG)(DG)(DA)(DA)(DG)(DC)(DT)(DT) (DC)(DC) (DA)(DC)(DC)(DG)(DA)(DA)(DC) (DG)(DT)(DA)(DT)(DG)(DT)(DA)(DC)(DC)(DC) (DG)(DG)(DA) (DA)(DG)(DA)(DC)(DG)(DG) (DT)(DG)(DC)(DT)(DC)(DT)(DG)(DA)(DA)(DA) (DG)(DG)(DT)(DG) (DA)(DA)(DA)(DT)(DC) (DA)(DA)(DA)(DA)(DT)(DG)(DC)(DG)(DT)(DC) (DT)(DG)(DA)(DA)(DA) (DC)(DT)(DG)(DA) (DA)(DA)(DG)(DA)(DC)(DG)(DG)(DT)(DG)(DG) (DT)(DC)(DA)(DC)(DT)(DA) (DC)(DG)(DA) (DC)(DG)(DC)(DT)(DG)(DA)(DA)(DG)(DT)(DT) (DA)(DA)(DA)(DA)(DC)(DC)(DA) (DC)(DC) (DT)(DA)(DC)(DA)(DT)(DG)(DG)(DC)(DT)(DA) (DA)(DA)(DA)(DA)(DA)(DC)(DC)(DG) (DG) (DT)(DT)(DC)(DA)(DG)(DC)(DT)(DG)(DC)(DC) (DG)(DG)(DG)(DT)(DG)(DC)(DT)(DT)(DA) (DC)(DA)(DA)(DA)(DA)(DC)(DC)(DG)(DA)(DC) (DA)(DT)(DC)(DA)(DA)(DA)(DC)(DT)(DG)(DG) (DA)(DC)(DA)(DT)(DC)(DA)(DC)(DC)(DT) (DC)(DC)(DC)(DA)(DC)(DA)(DA)(DC)(DG)(DA) (DA) (DG)(DA)(DC)(DT)(DA)(DC)(DA)(DC) (DC)(DA)(DT)(DC)(DG)(DT)(DT)(DG)(DA)(DA) (DC)(DA) (DG)(DT)(DA)(DC)(DG)(DA)(DA) (DC)(DG)(DT)(DG)(DC)(DT)(DG)(DA)(DA)(DG) (DG)(DT)(DC) (DG)(DT)(DC)(DA)(DC)(DT) (DC)(DC)(DA)(DC)(DC)(DG)(DG)(DT)(DG)(DC) (DT)(DT)(DA)(DA) (DT)(DA)(DA)(DC)(DG) (DC)(DT)(DG)(DA)(DT)(DA)(DG)(DT)(DG)(DC) (DT)(DA)(DG)(DT)(DG) (DT)(DA)(DG)(DA) (DT)(DC)(DG)(DC)(DT)(DA)(DC)(DT)(DA)(DG) (DA)(DG)(DC)(DC)(DA)(DG) (DG)(DC)(DA) (DT)(DC)(DA)(DA)(DA)(DT)(DA)(DA)(DA)(DA) (DC)(DG)(DA)(DA)(DA)(DG)(DG) (DC)(DT) (DC)(DA)(DG)(DT)(DC)(DG)(DA)(DA)(DA)(DG) (DA)(DC)(DT)(DG)(DG)(DG)(DC)(DC) (DT) (DT)(DT)(DC)(DG)(DT)(DT)(DT)(DT)(DA)(DT) (DC)(DT)(DG)(DT)(DT)(DG)(DT)(DT)(DT) (DG)(DT)(DC)(DG)(DG)(DT)(DG)(DA)(DA)(DC) (DG)(DC)(DT)(DC)(DT)(DC)(DT)(DA)(DC)(DT) (DA)(DG)(DA)(DG)(DT)(DC)(DA)(DC)(DA) (DC)(DT)(DG)(DG)(DC)(DT)(DC)(DA)(DC)(DC) (DT) (DT)(DC)(DG)(DG)(DG)(DT)(DG)(DG) (DG)(DC)(DC)(DT)(DT)(DT)(DC)(DT)(DG)(DC) (DG)(DT) (DT)(DT)(DA)(DT)(DA)(DC)(DG) (DT)(DC)(DT)(DC)(DT)(DC)(DA)(DT)(DT)(DG) (DA)(DC)(DC) (DG)(DG)(DG)(DA)(DG)(DC) (DG)(DC)(DC)(DC)(DT)(DG)(DT)(DA)(DG)(DC) (DG)(DG)(DC)(DG) (DC)(DA)(DT)(DT)(DA) (DA)(DG)(DC)(DG)(DC)(DG)(DG)(DC)(DG)(DG) (DG)(DT)(DG)(DT)(DG) (DG)(DT)(DG)(DG) (DT)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DA)(DG) (DC)(DG)(DT)(DG)(DA)(DC) (DC)(DG)(DC) (DT)(DA)(DC)(DA)(DC)(DT)(DT)(DG)(DC)(DC) (DA)(DG)(DC)(DG)(DC)(DC)(DC) (DT)(DA) (DG)(DC)(DG)(DC)(DC)(DC)(DG)(DC)(DT)(DC) (DC)(DC)(DG)(DG)(DG)(DA)(DT)(DC) (DG) (DG)(DA)(DA)(DT)(DT)(DC)(DC)(DG)(DG)(DC) (DC)(DA)(DT)(DC)(DG)(DC)(DC)(DC)(DT) (DG)(DA)(DT)(DA)(DG)(DA)(DC)(DG)(DG)(DT) (DT)(DT)(DT)(DT)(DC)(DG)(DC)(DC)(DC)(DT) (DT)(DT)(DG)(DA)(DC)(DG)(DT)(DT)(DG) (DG)(DA)(DG)(DT)(DC)(DC)(DA)(DC)(DG)(DT) (DT) (DC)(DT)(DT)(DT)(DA)(DA)(DT)(DA) (DG)(DT)(DG)(DG)(DA)(DC)(DT)(DC)(DT)(DT) (DG)(DT) (DT)(DC)(DC)(DA)(DA)(DA)(DC) (DT)(DG)(DG)(DA)(DA)(DC)(DA)(DA)(DC)(DA) (DC)(DT)(DC) (DA)(DA)(DC)(DC)(DC)(DT) (DA)(DT)(DC)(DT)(DC)(DG)(DG)(DG)(DC)(DA) (DA)(DG)(DC)(DT) (DT)(DG)(DT)(DC)(DA) (DC)(DA)(DG)(DA)(DG)(DA)(DC)(DG)(DC)(DA) (DA)(DT)(DA)(DC)(DG) (DC)(DA)(DA)(DA) (DC)(DC)(DG)(DC)(DC)(DT)(DC)(DT)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DC) (DG)(DT)(DT) (DG)(DG)(DC)(DC)(DG)(DA)(DT)(DT)(DC)(DA) (DT)(DT)(DA)(DA)(DT)(DG)(DC) (DA)(DG) (DC)(DT)(DG)(DG)(DC)(DA)(DC)(DG)(DA)(DC) (DA)(DG)(DG)(DT)(DT)(DT)(DC)(DC) (DC) (DG)(DA)(DC)(DT)(DG)(DG)(DA)(DA)(DA)(DG) (DC)(DG)(DG)(DG)(DC)(DA)(DG)(DT)(DG) (DA)(DG)(DC)(DG)(DC)(DA)(DA)(DC)(DG)(DC) (DA)(DA)(DT)(DT)(DA)(DA)(DT)(DG)(DT)(DG) (DA)(DG)(DT)(DT)(DA)(DG)(DC)(DT)(DC) (DA)(DC)(DT)(DC)(DA)(DT)(DT)(DA)(DG)(DG) (DC) (DA)(DC)(DC)(DC)(DC)(DA)(DG)(DG) (DC)(DT)(DT)(DT)(DA)(DC)(DA)(DC)(DT)(DT) (DT)(DA) (DT)(DG)(DC)(DT)(DT)(DC)(DC) (DG)(DG)(DC)(DT)(DC)(DG)(DT)(DA)(DT)(DG) (DT)(DT)(DG) (DT)(DG)(DT)(DG)(DG)(DA) (DA)(DT)(DT)(DG)(DT)(DG)(DA)(DG)(DC)(DG) (DG)(DA)(DT)(DA) (DA)(DC)(DA)(DA)(DT) (DT)(DT)(DC)(DA)(DC)(DA)(DC)(DA)(DT)(DA) (DC)(DT)(DA)(DG)(DA) (DG)(DA)(DA)(DA) (DG)(DA)(DG)(DG)(DA)(DG)(DA)(DA)(DA)(DT) (DA)(DC)(DT)(DA)(DG)(DA) (DT)(DG)(DG) (DC)(DT)(DT)(DC)(DC)(DT)(DC)(DC)(DG)(DA) (DA)(DG)(DA)(DC)(DG)(DT)(DT) (DA)(DT) (DC)(DA)(DA)(DA)(DG)(DA)(DG)(DT)(DT)(DC) (DA)(DT)(DG)(DC)(DG)(DT)(DT)(DT) (DC) (DA)(DA)(DA)(DG)(DT)(DT)(DC)(DG)(DT)(DA) (DT)(DG)(DG)(DA)(DA)(DG)(DG)(DT)(DT) (DC)(DC)(DG)(DT)(DT)(DA)(DA)(DC)(DG)(DG) (DT)(DC)(DA)(DC)(DG)(DA)(DG)(DT)(DT)(DC) (DG)(DA)(DA)(DA)(DT)(DC)(DG)(DA)(DA) (DG)(DG)(DT)(DG)(DA)(DA)(DG)(DG)(DT)(DG) (DA) (DA)(DG)(DG)(DT)(DC)(DG)(DT)(DC) (DC)(DG)(DT)(DA)(DC)(DG)(DA)(DA)(DG)(DG) (DT)(DA) (DC)(DC)(DC)(DA)(DG)(DA)(DC) (DC)(DG)(DC)(DT)(DA)(DA)(DA)(DC)(DT)(DG) (DA)(DA)(DA) (DG)(DT)(DT)(DA)(DC)(DC) (DA)(DA)(DA)(DG)(DG)(DT)(DG)(DG)(DT)(DC) (DC)(DG)(DC)(DT) (DG)(DC)(DC)(DG)(DT) (DT)(DC)(DG)(DC)(DT)(DT)(DG)(DG)(DG)(DA) (DC)(DA)(DT)(DC)(DC) (DT)(DG)(DT)(DC) (DC)(DC)(DC)(DG)(DC)(DA)(DG)(DT)(DT)(DC) (DC)(DA)(DG)(DT)(DA)(DC) (DG)(DG)(DT) (DT)(DC)(DC)(DA)(DA)(DA)(DG)(DC)(DT)(DT) (DA)(DC)(DG)(DT)(DT)(DA)(DA) (DA)(DC) (DA)(DC)(DC)(DC)(DG)(DG)(DC)(DT)(DG)(DA) (DC)(DA)(DT)(DC)(DC)(DC)(DG)(DG) (DA) (DC)(DT)(DA)(DC)(DC)(DT)(DG)(DA)(DA)(DA) (DC)(DT)(DG)(DT)(DC)(DC)(DT)(DT)(DC) (DC)(DC)(DG)(DG)(DA)(DA)(DG)(DG)(DT)(DT) (DT)(DC)(DA)(DA)(DA)(DT)(DG)(DG)(DG)(DA) (DA)(DC)(DG)(DT)(DG)(DT)(DT)(DA)(DT) (DG)(DA)(DA)(DC)(DT)(DT)(DC)(DG)(DA)(DA) (DG) (DA)(DC)(DG)(DG)(DT)(DG)(DG)(DT) (DG)(DT)(DT)(DG)(DT)(DT)(DA)(DC)(DC)(DG) (DT)(DT) (DA)(DC)(DC)(DC)(DA)(DG)(DG) (DA)(DC)(DT)(DC)(DC)(DT)(DC)(DC)(DC)(DT) (DG)(DC)(DA) (DA)(DG)(DA)(DC)(DG)(DG) (DT)(DG)(DA)(DG)(DT)(DT)(DC)(DA)(DT)(DC) (DT)(DA)(DC)(DA) (DA)(DA)(DG)(DT)(DT) (DA)(DA)(DA)(DC)(DT)(DG)(DC)(DG)(DT)(DG) (DG)(DT)

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Macromolecule #2: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.179719 KDa
SequenceString:
(DC)(DG)(DT)(DC)(DA)(DA)(DA)(DG)(DG)(DA) (DA)(DC)(DG)(DC)(DG)(DC)(DG)(DG)(DG)(DG) (DA)(DG)(DC)(DT)(DT)(DG)(DC)(DC)(DC) (DG)(DA)(DG)(DA)(DT)(DA)(DC)(DT)(DC)(DT) (DA) (DG)(DT)(DA)(DG)(DC)(DT)(DT)(DT) (DG)

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Macromolecule #3: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.015315 KDa
SequenceString:
(DA)(DC)(DT)(DC)(DC)(DA)(DA)(DG)(DT)(DG) (DT)(DT)(DG)(DT)(DT)(DC)(DC)(DA)(DG)(DT) (DT)(DG)(DT)(DC)(DT)(DG)(DG)(DG)(DA) (DC)(DT)(DG)(DC)(DG)(DG)(DG)(DT)(DG)(DT) (DA) (DG)(DT)

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Macromolecule #4: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.179561 KDa
SequenceString:
(DC)(DC)(DA)(DC)(DT)(DA)(DT)(DT)(DA)(DA) (DA)(DG)(DA)(DA)(DC)(DG)(DT)(DG)(DG)(DT) (DC)(DA)(DG)(DG)(DG)(DC)(DT)(DA)(DT) (DC)(DC)(DG)(DG)

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Macromolecule #5: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.243308 KDa
SequenceString:
(DT)(DG)(DC)(DG)(DT)(DC)(DT)(DC)(DT)(DT) (DA)(DT)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC) (DT)(DA)(DA)(DC)(DA)(DG)(DA)

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Macromolecule #6: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.700913 KDa
SequenceString:
(DC)(DG)(DA)(DA)(DC)(DT)(DC)(DA)(DC)(DA) (DT)(DT)(DA)(DA)(DC)(DT)(DG)(DC)(DA)(DT) (DT)(DA)(DA)(DT)(DG)(DA)(DA)(DT)(DC) (DG)(DG)(DC)(DC)(DG)(DC)

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Macromolecule #7: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.145745 KDa
SequenceString:
(DT)(DG)(DT)(DT)(DT)(DA)(DA)(DT)(DT)(DC) (DC)(DG)(DG)(DG)(DG)(DA)(DG)(DA)(DC)(DG) (DT)(DA)(DT)(DA)(DA)(DA)(DC)(DG)(DC) (DA)(DG)(DA)(DA)(DG)(DG)(DT)(DC)(DC)(DC) (DA) (DT)(DT)(DT)(DG)(DA)(DA)(DA)(DC) (DC)

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Macromolecule #8: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.520758 KDa
SequenceString:
(DG)(DA)(DT)(DG)(DT)(DC)(DA)(DT)(DA)(DC) (DT)(DG)(DG)(DA)(DT)(DA)(DC)(DC)(DT)(DT) (DC)(DG)(DT)(DA)(DC)(DG)(DT)(DG)(DG) (DG)(DT)(DT)(DG)(DA)

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Macromolecule #9: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.51575 KDa
SequenceString:
(DC)(DA)(DA)(DG)(DT)(DG)(DG)(DA)(DT)(DG) (DG)(DC)(DC)(DG)(DG)(DA)(DA)(DT)(DT)(DC) (DC)(DG)(DA)(DT)(DC)(DC)(DC)(DG)(DG) (DG)(DA)(DT)(DT)(DT)

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Macromolecule #10: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 10 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.214927 KDa
SequenceString:
(DT)(DT)(DT)(DG)(DC)(DG)(DG)(DG)(DC)(DG) (DC)(DT)(DA)(DG)(DG)(DG)(DT)(DA)(DA)(DC) (DC)(DA)(DC)(DC)(DA)(DC)(DA)(DT)(DT) (DT)

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Macromolecule #11: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 11 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.125035 KDa
SequenceString:
(DT)(DT)(DT)(DC)(DC)(DA)(DG)(DT)(DC)(DG) (DG)(DG)(DA)(DA)(DA)(DC)(DC)(DT)(DG)(DT) (DC)(DG)(DT)(DG)(DC)(DC)(DA)(DG)(DT) (DT)(DG)(DC)(DG)(DT)(DA)(DC)(DA)(DC)(DG) (DT) (DA)(DG)(DT)(DC)(DC)(DT)

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Macromolecule #12: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 12 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.171109 KDa
SequenceString:
(DG)(DG)(DG)(DT)(DA)(DA)(DC)(DA)(DC)(DC) (DG)(DT)(DC)(DT)(DT)(DA)(DA)(DA)(DA)(DC) (DG)(DT)(DT)(DA)(DT)(DT)(DT)(DG)(DA) (DT)(DG)(DC)(DC)(DT)(DG)(DG)(DT)(DA)(DC) (DA) (DT)(DA)(DC)(DG)(DT)(DT)

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Macromolecule #13: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.500614 KDa
SequenceString:
(DT)(DT)(DT)(DC)(DC)(DC)(DG)(DC)(DC)(DG) (DC)(DG)(DC)(DT)(DT)(DA)(DA)(DT)(DG)(DC) (DG)(DC)(DA)(DG)(DT)(DT)(DT)(DG)(DA) (DT)(DG)(DT)(DC)(DG)(DG)(DT)(DT)(DT)(DT) (DG) (DT)(DT)(DT)(DT)

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Macromolecule #14: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 14 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.826682 KDa
SequenceString:
(DT)(DT)(DT)(DA)(DC)(DC)(DG)(DT)(DC)(DT) (DT)(DC)(DG)(DA)(DA)(DG)(DT)(DT)(DC)(DA) (DT)(DA)(DT)(DG)(DC)(DG)(DC)(DT)(DC)

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Macromolecule #15: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 15 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.427979 KDa
SequenceString:
(DA)(DA)(DG)(DG)(DA)(DC)(DA)(DG)(DT)(DT) (DT)(DC)(DA)(DG)(DG)(DT)(DA)(DG)(DG)(DC) (DA)(DG)(DG)(DG)(DC)(DG)(DC)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DC)(DA)(DA)(DT)(DG) (DA)

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Macromolecule #16: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 16 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.235442 KDa
SequenceString:
(DG)(DG)(DT)(DC)(DA)(DC)(DG)(DC)(DT)(DG) (DC)(DG)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DG) (DG)(DA)(DT)(DG)(DT)(DC)(DC)(DT)(DT) (DT)(DC)(DA)(DG)(DT)(DT)(DC)(DG)(DA)(DA) (DC) (DT)(DC)(DG)

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Macromolecule #17: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 17 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.224841 KDa
SequenceString:
(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DA)(DC)(DC) (DC)(DG)(DG)(DC)(DA)(DG)(DC)(DT)(DG)(DA) (DA)(DC)(DC)(DG)(DG)(DT)(DT)(DT)(DA) (DT)(DG)(DT)(DC)(DC)(DC)(DG)(DC)(DT)(DA) (DC)

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Macromolecule #18: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 18 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.196952 KDa
SequenceString:
(DT)(DT)(DT)(DG)(DT)(DA)(DG)(DA)(DT)(DG) (DA)(DA)(DC)(DT)(DC)(DG)(DG)(DT)(DA)(DA) (DC)(DA)(DA)(DC)(DA)(DC)(DC)(DT)(DT) (DT)

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Macromolecule #19: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 19 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.470732 KDa
SequenceString:
(DT)(DG)(DC)(DA)(DG)(DG)(DA)(DG)(DT)(DT) (DG)(DG)(DT)(DA)(DC)(DC)(DA)(DC)(DG)(DC) (DA)(DG)(DT)(DT)(DT)(DA)(DA)(DC)(DT) (DT)(DT)(DT)(DT)(DT)

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Macromolecule #20: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 20 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.517002 KDa
SequenceString:
(DC)(DC)(DA)(DG)(DT)(DG)(DT)(DG)(DT)(DT) (DG)(DT)(DG)(DG)(DG)(DA)(DG)(DG)(DT)(DG) (DT)(DT)(DT)(DA)(DG)(DC)(DC)(DA)(DT) (DG)(DT)(DA)(DG)(DG)(DT)(DG)(DG)(DT)(DT) (DA)

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Macromolecule #21: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 21 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 13.099423 KDa
SequenceString:
(DG)(DA)(DG)(DG)(DA)(DA)(DG)(DC)(DC)(DA) (DT)(DC)(DA)(DA)(DA)(DT)(DT)(DG)(DT)(DG) (DT)(DG)(DA)(DC)(DA)(DA)(DG)(DA)(DG) (DG)(DC)(DG)(DG)(DT)(DT)(DT)(DG)(DC)(DG) (DT) (DA)(DT)

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Macromolecule #22: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 22 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.30727 KDa
SequenceString:
(DC)(DT)(DT)(DC)(DC)(DA)(DT)(DG)(DT)(DT) (DA)(DT)(DT)(DA)(DT)(DC)(DA)(DG)(DA)(DC) (DG)(DT)(DC)(DG)(DT)(DA)(DG)(DT)(DG) (DA)(DC)(DC)(DA)(DC)(DC)(DG)(DT)

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Macromolecule #23: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 23 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.705178 KDa
SequenceString:
(DT)(DG)(DA)(DC)(DC)(DG)(DT)(DT)(DA)(DA) (DC)(DG)(DG)(DA)(DA)(DC)(DT)(DT)(DC)(DG) (DA)(DT)(DT)(DT)(DT)(DA)(DG)(DC)(DG) (DT)(DG)(DG)(DA)(DA)(DC)(DA)(DA)(DG)(DA) (DG) (DT)

+
Macromolecule #24: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 24 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.087481 KDa
SequenceString:
(DG)(DT)(DT)(DC)(DA)(DC)(DC)(DG)(DT)(DA) (DG)(DC)(DG)(DA)(DC)(DT)(DC)(DT)(DT)(DT) (DG)(DA)(DT)(DA)(DA)(DC)(DG)(DT)(DC) (DT)(DT)(DC)(DG)

+
Macromolecule #25: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 25 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.903008 KDa
SequenceString:
(DA)(DG)(DA)(DG)(DA)(DG)(DC)(DA)(DG)(DG) (DT)(DG)(DA)(DG)(DT)(DA)(DA)(DC)(DC)(DG) (DG)(DA)(DC)(DC)(DG)(DT)(DC)(DG)(DC) (DA)(DT)(DG)(DG)(DT)(DT)

+
Macromolecule #26: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 26 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 9.571176 KDa
SequenceString:
(DT)(DC)(DT)(DA)(DG)(DT)(DG)(DA)(DA)(DC) (DC)(DG)(DG)(DC)(DC)(DG)(DG)(DG)(DG)(DA) (DA)(DA)(DA)(DA)(DC)(DC)(DG)(DT)(DC) (DT)(DA)

+
Macromolecule #27: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 27 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.872563 KDa
SequenceString:
(DC)(DT)(DT)(DC)(DG)(DA)(DC)(DT)(DA)(DT) (DC)(DA)(DG)(DC)(DA)(DC)(DG)(DA)(DA)(DC) (DT)(DT)(DT)(DG)(DA)(DA)(DA)(DC)(DT) (DT)(DG)(DA)(DC)(DG)(DA)(DC)(DC)(DT)(DT) (DC) (DA)(DC)(DC)(DT)(DT)(DC)(DA)(DC) (DC)

+
Macromolecule #28: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 28 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.713506 KDa
SequenceString:
(DT)(DT)(DT)(DA)(DC)(DG)(DT)(DT)(DC)(DG) (DT)(DA)(DC)(DT)(DG)(DT)(DT)(DC)(DA)(DG) (DG)(DT)(DG)(DG)(DA)(DG)(DT)(DG)(DA) (DC)(DG)(DA)(DC)(DC)(DT)(DT)(DT)(DT)

+
Macromolecule #29: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 29 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.722431 KDa
SequenceString:
(DT)(DT)(DT)(DG)(DA)(DC)(DT)(DG)(DA)(DG) (DC)(DC)(DT)(DT)(DT)(DC)(DG)(DT)(DT)(DA) (DA)(DA)(DG)(DG)(DC)(DC)(DG)(DT)(DG) (DT)(DA)(DA)(DA)(DA)(DC)(DT)(DG)(DC)(DC) (DC) (DG)(DC)(DT)(DT)(DT)(DT)(DT)(DT)

+
Macromolecule #30: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 30 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.670501 KDa
SequenceString:
(DT)(DT)(DT)(DG)(DA)(DC)(DC)(DA)(DC)(DC) (DT)(DT)(DT)(DG)(DG)(DT)(DA)(DA)(DC)(DC) (DA)(DA)(DG)(DC)(DG)(DA)(DA)(DC)(DG) (DG)(DC)(DA)(DG)(DC)(DG)(DT)(DT)(DT)

+
Macromolecule #31: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 31 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.256343 KDa
SequenceString:
(DT)(DT)(DT)(DC)(DG)(DG)(DA)(DA)(DG)(DC) (DA)(DT)(DA)(DA)(DA)(DC)(DA)(DG)(DT)(DC) (DT)(DT)(DT)(DC)(DT)(DT)(DT)

+
Macromolecule #32: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 32 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.966068 KDa
SequenceString:
(DG)(DC)(DC)(DT)(DG)(DG)(DG)(DC)(DT)(DC) (DA)(DC)(DA)(DA)(DT)(DT)(DC)(DC)(DA)(DC) (DA)(DC)(DA)(DA)(DC)(DA)(DT)(DA)(DC) (DG)(DA)(DG)(DC)(DT)(DT)(DT)

+
Macromolecule #33: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 33 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.886285 KDa
SequenceString:
(DG)(DA)(DG)(DC)(DT)(DT)(DA)(DA)(DT)(DG) (DT)(DG)(DT)(DG)(DT)(DA)(DG)(DT)(DA)(DT) (DT)(DT)(DC)(DT)(DC)(DC)(DT)(DC)(DG) (DC)(DA)(DT)(DG)(DA)(DA)(DT)(DC)(DT)(DA) (DC) (DA)(DC)

+
Macromolecule #34: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 34 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 10.741924 KDa
SequenceString:
(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DT)(DC)(DT) (DT)(DC)(DC)(DG)(DG)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DA)(DC)(DA)(DA)(DA)(DC)(DA) (DA)(DT)(DG)(DA)(DG)(DT)

+
Macromolecule #35: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 35 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 14.607367 KDa
SequenceString:
(DC)(DT)(DT)(DT)(DC)(DA)(DG)(DT)(DT)(DT) (DT)(DT)(DC)(DT)(DG)(DC)(DT)(DT)(DA)(DA) (DC)(DT)(DT)(DC)(DA)(DG)(DC)(DG)(DC) (DA)(DT)(DT)(DT)(DT)(DG)(DA)(DT)(DT)(DT) (DC) (DA)(DC)(DT)(DA)(DG)(DC)(DA)(DC)

+
Macromolecule #36: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 36 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 8.301359 KDa
SequenceString:
(DC)(DT)(DT)(DT)(DC)(DA)(DG)(DT)(DT)(DA) (DG)(DC)(DA)(DC)(DC)(DA)(DC)(DG)(DA)(DT) (DG)(DG)(DG)(DA)(DC)(DA)(DG)

+
Macromolecule #37: DNA Staple

MacromoleculeName: DNA Staple / type: dna / ID: 37 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 12.327908 KDa
SequenceString:
(DC)(DG)(DG)(DT)(DG)(DG)(DA)(DA)(DG)(DC) (DT)(DT)(DC)(DC)(DC)(DA)(DA)(DC)(DC)(DG) (DA)(DC)(DG)(DG)(DG)(DA)(DG)(DA)(DA) (DG)(DG)(DC)(DC)(DC)(DA)(DC)(DC)(DC)(DG) (DA)

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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 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
DetailsMonodisperse, 20nM

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 10.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44605
FSC plot (resolution estimation)

-
Atomic model buiding 1

DetailsInitial model generated by ENRG-MD. Then MDFF in combination with the ENRG-MD elastic network was used for flexible fitting.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7arq:
Cryo EM of 3D DNA origami 16 helix bundle

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