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Open data
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Basic information
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Title | Six DNA Helix Bundle nanopore - State 3 | |||||||||||||||
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![]() | DNA origami / nanopore. / DNA | |||||||||||||||
Biological species | DNA molecule (others) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.0 Å | |||||||||||||||
![]() | Javed A / Ahmad K | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations. Authors: Katya Ahmad / Abid Javed / Conor Lanphere / Peter V Coveney / Elena V Orlova / Stefan Howorka / ![]() ![]() Abstract: DNA can be folded into rationally designed, unique, and functional materials. To fully realise the potential of these DNA materials, a fundamental understanding of their structure and dynamics is ...DNA can be folded into rationally designed, unique, and functional materials. To fully realise the potential of these DNA materials, a fundamental understanding of their structure and dynamics is necessary, both in simple solvents as well as more complex and diverse anisotropic environments. Here we analyse an archetypal six-duplex DNA nanoarchitecture with single-particle cryo-electron microscopy and molecular dynamics simulations in solvents of tunable ionic strength and within the anisotropic environment of biological membranes. Outside lipid bilayers, the six-duplex bundle lacks the designed symmetrical barrel-type architecture. Rather, duplexes are arranged in non-hexagonal fashion and are disorted to form a wider, less elongated structure. Insertion into lipid membranes, however, restores the anticipated barrel shape due to lateral duplex compression by the bilayer. The salt concentration has a drastic impact on the stability of the inserted barrel-shaped DNA nanopore given the tunable electrostatic repulsion between the negatively charged duplexes. By synergistically combining experiments and simulations, we increase fundamental understanding into the environment-dependent structural dynamics of a widely used nanoarchitecture. This insight will pave the way for future engineering and biosensing applications. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 51.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.4 KB 17.4 KB | Display Display | ![]() |
Images | ![]() | 26.1 KB | ||
Filedesc metadata | ![]() | 5.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 419.7 KB | Display | ![]() |
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Full document | ![]() | 419.3 KB | Display | |
Data in XML | ![]() | 6.6 KB | Display | |
Data in CIF | ![]() | 7.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ywlMC ![]() 7ywhC ![]() 7ywiC ![]() 7ywnC ![]() 7ywoC M: atomic model generated by this map C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Six DNA helix bundle DNA nanopore
Entire | Name: Six DNA helix bundle DNA nanopore |
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Components |
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-Supramolecule #1: Six DNA helix bundle DNA nanopore
Supramolecule | Name: Six DNA helix bundle DNA nanopore / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Macromolecule #1: DNA (50-MER)
Macromolecule | Name: DNA (50-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: DNA molecule (others) |
Molecular weight | Theoretical: 15.334821 KDa |
Sequence | String: (DA)(DG)(DC)(DG)(DA)(DA)(DC)(DG)(DT)(DG) (DG)(DA)(DT)(DT)(DT)(DT)(DG)(DT)(DC)(DC) (DG)(DA)(DC)(DA)(DT)(DC)(DG)(DG)(DC) (DA)(DA)(DG)(DC)(DT)(DC)(DC)(DC)(DT)(DT) (DT) (DT)(DT)(DC)(DG)(DA)(DC)(DT)(DA) (DT)(DT) |
-Macromolecule #2: DNA (50-MER)
Macromolecule | Name: DNA (50-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: DNA molecule (others) |
Molecular weight | Theoretical: 15.413827 KDa |
Sequence | String: (DC)(DC)(DG)(DA)(DT)(DG)(DT)(DC)(DG)(DG) (DA)(DC)(DT)(DT)(DT)(DT)(DA)(DC)(DA)(DC) (DG)(DA)(DT)(DC)(DT)(DT)(DC)(DG)(DC) (DC)(DT)(DG)(DC)(DT)(DG)(DG)(DG)(DT)(DT) (DT) (DT)(DG)(DG)(DG)(DA)(DG)(DC)(DT) (DT)(DG) |
-Macromolecule #3: DNA (50-MER)
Macromolecule | Name: DNA (50-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: DNA molecule (others) |
Molecular weight | Theoretical: 15.285784 KDa |
Sequence | String: (DC)(DG)(DA)(DA)(DG)(DA)(DT)(DC)(DG)(DT) (DG)(DT)(DT)(DT)(DT)(DT)(DC)(DC)(DA)(DC) (DA)(DG)(DT)(DT)(DG)(DA)(DT)(DT)(DG) (DC)(DC)(DC)(DT)(DT)(DC)(DA)(DC)(DT)(DT) (DT) (DT)(DC)(DC)(DC)(DA)(DG)(DC)(DA) (DG)(DG) |
-Macromolecule #4: DNA (50-MER)
Macromolecule | Name: DNA (50-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: DNA molecule (others) |
Molecular weight | Theoretical: 15.483923 KDa |
Sequence | String: (DA)(DA)(DT)(DC)(DA)(DA)(DC)(DT)(DG)(DT) (DG)(DG)(DT)(DT)(DT)(DT)(DT)(DC)(DT)(DC) (DA)(DC)(DT)(DG)(DG)(DT)(DG)(DA)(DT) (DT)(DA)(DG)(DA)(DA)(DT)(DG)(DC)(DT)(DT) (DT) (DT)(DG)(DT)(DG)(DA)(DA)(DG)(DG) (DG)(DC) |
-Macromolecule #5: DNA (50-MER)
Macromolecule | Name: DNA (50-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: DNA molecule (others) |
Molecular weight | Theoretical: 15.403877 KDa |
Sequence | String: (DT)(DC)(DA)(DC)(DC)(DA)(DG)(DT)(DG)(DA) (DG)(DA)(DT)(DT)(DT)(DT)(DT)(DG)(DT)(DC) (DG)(DT)(DA)(DC)(DC)(DA)(DG)(DG)(DT) (DG)(DC)(DA)(DT)(DG)(DG)(DA)(DT)(DT)(DT) (DT) (DT)(DG)(DC)(DA)(DT)(DT)(DC)(DT) (DA)(DA) |
-Macromolecule #6: DNA (50-MER)
Macromolecule | Name: DNA (50-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: DNA molecule (others) |
Molecular weight | Theoretical: 15.268795 KDa |
Sequence | String: (DC)(DC)(DT)(DG)(DG)(DT)(DA)(DC)(DG)(DA) (DC)(DA)(DT)(DT)(DT)(DT)(DT)(DC)(DC)(DA) (DC)(DG)(DT)(DT)(DC)(DG)(DC)(DT)(DA) (DA)(DT)(DA)(DG)(DT)(DC)(DG)(DA)(DT)(DT) (DT) (DT)(DA)(DT)(DC)(DC)(DA)(DT)(DG) (DC)(DA) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.4 / Component - Concentration: 12.0 mM / Component - Formula: MgCl2 / Component - Name: Magnesium Chloride |
Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 1.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Calibrated magnification: 47000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Sample stage | Specimen 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
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation |
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Output model | ![]() PDB-7ywl: |