[English] 日本語
Yorodumi
- EMDB-16076: Helical shell of CCMV capsid protein on DNA origami 6HB-2k -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16076
TitleHelical shell of CCMV capsid protein on DNA origami 6HB-2k
Map data
Sample
  • Complex: Helical shell of CCMV capsid protein on DNA origami 6HB-2k
    • Protein or peptide: Coat protein
Keywordsorigami / capsid / VIRUS LIKE PARTICLE
Function / homologyBromovirus coat protein / Bromovirus coat protein / viral capsid / structural molecule activity / Coat protein
Function and homology information
Biological speciesCowpea chlorotic mottle virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsKumpula E-P / Seitz I / Kostiainen MA / Huiskonen JT
Funding supportEuropean Union, Finland, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)101002258European Union
Academy of Finland341057 Finland
CitationJournal: Nat Nanotechnol / Year: 2023
Title: DNA-origami-directed virus capsid polymorphism.
Authors: Iris Seitz / Sharon Saarinen / Esa-Pekka Kumpula / Donna McNeale / Eduardo Anaya-Plaza / Vili Lampinen / Vesa P Hytönen / Frank Sainsbury / Jeroen J L M Cornelissen / Veikko Linko / Juha T ...Authors: Iris Seitz / Sharon Saarinen / Esa-Pekka Kumpula / Donna McNeale / Eduardo Anaya-Plaza / Vili Lampinen / Vesa P Hytönen / Frank Sainsbury / Jeroen J L M Cornelissen / Veikko Linko / Juha T Huiskonen / Mauri A Kostiainen /
Abstract: Viral capsids can adopt various geometries, most iconically characterized by icosahedral or helical symmetries. Importantly, precise control over the size and shape of virus capsids would have ...Viral capsids can adopt various geometries, most iconically characterized by icosahedral or helical symmetries. Importantly, precise control over the size and shape of virus capsids would have advantages in the development of new vaccines and delivery systems. However, current tools to direct the assembly process in a programmable manner are exceedingly elusive. Here we introduce a modular approach by demonstrating DNA-origami-directed polymorphism of single-protein subunit capsids. We achieve control over the capsid shape, size and topology by employing user-defined DNA origami nanostructures as binding and assembly platforms, which are efficiently encapsulated within the capsid. Furthermore, the obtained viral capsid coatings can shield the encapsulated DNA origami from degradation. Our approach is, moreover, not limited to a single type of capsomers and can also be applied to RNA-DNA origami structures to pave way for next-generation cargo protection and targeting strategies.
History
DepositionNov 1, 2022-
Header (metadata) releaseJul 5, 2023-
Map releaseJul 5, 2023-
UpdateOct 25, 2023-
Current statusOct 25, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16076.png

Downloads & links

-
Map

FileDownload / File: emd_16076.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 512 pix.
= 491.52 Å		0.96 Å/pix.
x 512 pix.
= 491.52 Å		0.96 Å/pix.
x 512 pix.
= 491.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 12.0
Minimum - Maximum-89.379999999999995 - 130.52770000000001
Average (Standard dev.)-0.034542467 (±5.8795233)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 491.52 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_16076_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_16076_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_16076_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Helical shell of CCMV capsid protein on DNA origami 6HB-2k

EntireName: Helical shell of CCMV capsid protein on DNA origami 6HB-2k
Components
  • Complex: Helical shell of CCMV capsid protein on DNA origami 6HB-2k
    • Protein or peptide: Coat protein

-
Supramolecule #1: Helical shell of CCMV capsid protein on DNA origami 6HB-2k

SupramoleculeName: Helical shell of CCMV capsid protein on DNA origami 6HB-2k
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Cowpea chlorotic mottle virus

-
Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Cowpea chlorotic mottle virus
Molecular weightTheoretical: 20.336252 KDa
SequenceString:
MSTVGTGKLT RAQRRAAARK NKRNTRVVQP VIVEPIASGQ GKAIKAWTGY SVSKWTASCA AAEAKVTSAI TISLPNELSS ERNKQLKVG RVLLWLGLLP SVSGTVKSCV TETQTTAAAS FQVALAVADN SKDVVAAMYP EAFKGITLEQ LAADLTIYLY S SAALTEGD VIVHLEVEHV RPTFDDSFTP VY

UniProtKB: Coat protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 695465
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

-
Atomic model buiding 1

DetailsInitial model pdb:1cwp was first manually adjusted to density in ISOLDE and then refined in PHENIX
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8bi4:
Helical shell of CCMV capsid protein on DNA origami 6HB-2k

+
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