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- EMDB-14344: Six DNA Helix Bundle nanopore - State 3 -

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Basic information

Entry
Database: EMDB / ID: EMD-14344
TitleSix DNA Helix Bundle nanopore - State 3
Map data
Sample
  • Complex: Six DNA helix bundle DNA nanopore
    • DNA: DNA (50-MER)
    • DNA: DNA (50-MER)
    • DNA: DNA (50-MER)
    • DNA: DNA (50-MER)
    • DNA: DNA (50-MER)
    • DNA: DNA (50-MER)
KeywordsDNA origami / nanopore. / DNA
Biological speciesDNA molecule (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsJaved A / Ahmad K
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M012700/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M025373/1 United Kingdom
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
CitationJournal: Nat Commun / Year: 2023
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
DepositionFeb 14, 2022-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14344.png

Downloads & links

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Map

FileDownload / File: emd_14344.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.79
Minimum - Maximum-0.2158444 - 3.4366565
Average (Standard dev.)0.0070616025 (±0.07842012)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Six DNA helix bundle DNA nanopore

EntireName: Six DNA helix bundle DNA nanopore
Components
  • Complex: Six DNA helix bundle DNA nanopore
    • DNA: DNA (50-MER)
    • DNA: DNA (50-MER)
    • DNA: DNA (50-MER)
    • DNA: DNA (50-MER)
    • DNA: DNA (50-MER)
    • DNA: DNA (50-MER)

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Supramolecule #1: Six DNA helix bundle DNA nanopore

SupramoleculeName: Six DNA helix bundle DNA nanopore / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Macromolecule #1: DNA (50-MER)

MacromoleculeName: DNA (50-MER) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 15.334821 KDa
SequenceString:
(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)

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Macromolecule #2: DNA (50-MER)

MacromoleculeName: DNA (50-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 15.413827 KDa
SequenceString:
(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)

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Macromolecule #3: DNA (50-MER)

MacromoleculeName: DNA (50-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 15.285784 KDa
SequenceString:
(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)

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Macromolecule #4: DNA (50-MER)

MacromoleculeName: DNA (50-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 15.483923 KDa
SequenceString:
(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)

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Macromolecule #5: DNA (50-MER)

MacromoleculeName: DNA (50-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 15.403877 KDa
SequenceString:
(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)

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Macromolecule #6: DNA (50-MER)

MacromoleculeName: DNA (50-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: DNA molecule (others)
Molecular weightTheoretical: 15.268795 KDa
SequenceString:
(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)

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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

Concentration1 mg/mL
BufferpH: 7.4 / Component - Concentration: 12.0 mM / Component - Formula: MgCl2 / Component - Name: Magnesium Chloride
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 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

Particle selectionNumber selected: 368501
Startup modelType of model: INSILICO MODEL
Details: Obtained using Ab-initio Reconstruction implemented in cryosparc.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: cryoSPARC (ver. 2.5) / Number images used: 24318
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.5)
Final 3D classificationNumber classes: 5 / Avg.num./class: 20000 / Software - Name: cryoSPARC (ver. 2.5)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation
Output model

PDB-7ywl:
Six DNA Helix Bundle nanopore - State 3

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