[English] 日本語
Yorodumi
- EMDB-16219: Triple-stranded DNA as a structural element in DNA origami large ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16219
TitleTriple-stranded DNA as a structural element in DNA origami large cuboid with TFO object
Map dataDNA origami object with triple - stranded DNA segment
Sample
  • Complex: DNA Nanostructure
    • Complex: Scaffold DNA single-strand
    • Complex: Staple oligonucleotides
KeywordsDNA Origami / Triplex forming Oligo / Triplex / TFO / large cuboid / large cuboid with TFO / DNA
Biological speciessynthetic construct (others) / Phage M13mp18 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.08 Å
AuthorsSachenbacher K / Khoshouei A / Honemann MN / Engelen W / Feigl E / Dietz H
Funding supportEuropean Union, Germany, Netherlands, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)101018465European Union
German Research Foundation (DFG) Germany
Netherlands Organisation for Scientific Research (NWO)019.182EN.037 Netherlands
European Union (EU)899619European Union
CitationJournal: Acs Nano / Year: 2023
Title: Triple-Stranded DNA As a Structural Element in DNA Origami
Authors: Sachenbacher K / Khoshouei A / Honemann MN / Engelen W / Feigl E / Dietz H
History
DepositionNov 23, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16219.png

Downloads & links

-
Map

FileDownload / File: emd_16219.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDNA origami object with triple - stranded DNA segment
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.1 Å/pix.
x 200 pix.
= 420. Å		2.1 Å/pix.
x 200 pix.
= 420. Å		2.1 Å/pix.
x 200 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0404
Minimum - Maximum-0.053635225 - 0.20306112
Average (Standard dev.)0.002786783 (±0.016143413)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: DNA origami object with triple - stranded DNA segment / half map 2

Fileemd_16219_half_map_1.map
AnnotationDNA origami object with triple - stranded DNA segment / half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: DNA origami object with triple - stranded DNA segment / half map 1

Fileemd_16219_half_map_2.map
AnnotationDNA origami object with triple - stranded DNA segment / half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : DNA Nanostructure

EntireName: DNA Nanostructure
Components
  • Complex: DNA Nanostructure
    • Complex: Scaffold DNA single-strand
    • Complex: Staple oligonucleotides

-
Supramolecule #1: DNA Nanostructure

SupramoleculeName: DNA Nanostructure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

-
Supramolecule #2: Scaffold DNA single-strand

SupramoleculeName: Scaffold DNA single-strand / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Phage M13mp18 (virus)

-
Supramolecule #3: Staple oligonucleotides

SupramoleculeName: Staple oligonucleotides / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: synthetic construct (others)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 5 / Details: 5 mM MES, 5mM NaCl and 5 mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 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

+
Image processing

Startup modelType of model: INSILICO MODEL / In silico model: de-novo generated initial model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110804
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

+
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