[English] 日本語
Yorodumi
- EMDB-14345: Six DNA Helix Bundle nanopore - State 4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14345
TitleSix DNA Helix Bundle nanopore - State 4
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 / Lanphere C / Orlova EV / Coveney P / Howorka S
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 5, 2023-
Current statusJul 5, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14345.png

Downloads & links

-
Map

FileDownload / File: emd_14345.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-0.25470045 - 3.574575
Average (Standard dev.)0.007164256 (±0.08027029)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Sample components

-
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)

-
Supramolecule #1: Six DNA helix bundle DNA nanopore

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

-
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)

-
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)

-
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)

-
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)

-
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)

-
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)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
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 FIELDBright-field microscopy / 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
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 368501
Startup modelType of model: INSILICO MODEL
Details: Obtained using Ab-initio Reconstruction implemented in cryosparc
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.5)
Final 3D classificationNumber classes: 5 / Avg.num./class: 20000 / Software - Name: cryoSPARC (ver. 2.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.5)
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: 27900

-
Atomic model buiding 1

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

PDB-7ywn:
Six DNA Helix Bundle nanopore - State 4

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more