[English] 日本語
Yorodumi
- EMDB-4899: Atlantic Cod Nervous Necrosis Virus-Like Particle produced in Nic... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4899
TitleAtlantic Cod Nervous Necrosis Virus-Like Particle produced in Nicotiana benthamiana
Map dataAtlantic Cod Nervous Necrosis Virus-Like Particle produced in Nicotiana benthamiana (local resolution filtered map).
Sample
  • Virus: Betanodavirus sp.
    • Protein or peptide: Coat protein
Function / homologyNodavirus capsid / nodavirus capsid protein / T=3 icosahedral viral capsid / Viral coat protein subunit / Capsid protein alpha
Function and homology information
Biological speciesBetanodavirus sp.
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHurdiss DL / Ranson NA
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/M027856/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBBS/E/J/000PR9794 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J004596/1 United Kingdom
Wellcome Trust102572/B/13/Z United Kingdom
CitationJournal: Front Plant Sci / Year: 2019
Title: Plant-Made Nervous Necrosis Virus-Like Particles Protect Fish Against Disease.
Authors: Johanna Marsian / Daniel L Hurdiss / Neil A Ranson / Anneli Ritala / Richard Paley / Irene Cano / George P Lomonossoff /
Abstract: Virus-like particles (VLPs) of the fish virus, Atlantic Cod Nervous necrosis virus (ACNNV), were successfully produced by transient expression of the coat protein in plants. VLPs could also be ...Virus-like particles (VLPs) of the fish virus, Atlantic Cod Nervous necrosis virus (ACNNV), were successfully produced by transient expression of the coat protein in plants. VLPs could also be produced in transgenic tobacco BY-2 cells. The protein extracted from plants self-assembled into = 3 particles, that appeared to be morphologically similar to previously analyzed NNV VLPs when analyzed by high resolution cryo-electron microscopy. Administration of the plant-produced VLPs to sea bass () showed that they could protect the fish against subsequent virus challenge, indicating that plant-produced vaccines may have a substantial future role in aquaculture.
History
DepositionApr 25, 2019-
Header (metadata) releaseJul 17, 2019-
Map releaseJul 17, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0138
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0138
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6rj0
  • Surface level: 0.0138
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6rj0
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4899.png

Downloads & links

-
Map

FileDownload / File: emd_4899.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAtlantic Cod Nervous Necrosis Virus-Like Particle produced in Nicotiana benthamiana (local resolution filtered map).
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.0138 / Movie #1: 0.0138
Minimum - Maximum-0.04114394 - 0.07030399
Average (Standard dev.)0.00027246008 (±0.004644915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z424.000424.000424.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0410.0700.000

-
Supplemental data

-
Additional map: Atlantic Cod Nervous Necrosis Virus-Like Particle produced in...

Fileemd_4899_additional.map
AnnotationAtlantic Cod Nervous Necrosis Virus-Like Particle produced in Nicotiana benthamiana (unsharpened map).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Atlantic Cod Nervous Necrosis Virus-Like Particle produced in...

Fileemd_4899_half_map_1.map
AnnotationAtlantic Cod Nervous Necrosis Virus-Like Particle produced in Nicotiana benthamiana (half map one).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Atlantic Cod Nervous Necrosis Virus-Like Particle produced in...

Fileemd_4899_half_map_2.map
AnnotationAtlantic Cod Nervous Necrosis Virus-Like Particle produced in Nicotiana benthamiana (half map two).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Betanodavirus sp.

EntireName: Betanodavirus sp.
Components
  • Virus: Betanodavirus sp.
    • Protein or peptide: Coat protein

-
Supramolecule #1: Betanodavirus sp.

SupramoleculeName: Betanodavirus sp. / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1906674 / Sci species name: Betanodavirus sp. / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Gadus morhua (Atlantic cod)
Host systemOrganism: Nicotiana benthamiana (plant)
Molecular weightTheoretical: 7.7 MDa
Virus shellShell ID: 1 / T number (triangulation number): 3

-
Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Betanodavirus sp.
Molecular weightTheoretical: 36.903711 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: VRKGNKKLAK QATTKAVNPQ PRRRNNNRRR GMRADAPLAK ASTITGFGRG TNDVHLTGMS RIAQAVIPAG TGTDGYIVVD ETIVPELLP RLGFAARIFQ RYAVETLEFE IQPMCPANTG GGYVAGFLPD PTDSDHTFDA IQATRGAVVA KWWESRTIRP Q YARALLWT ...String:
VRKGNKKLAK QATTKAVNPQ PRRRNNNRRR GMRADAPLAK ASTITGFGRG TNDVHLTGMS RIAQAVIPAG TGTDGYIVVD ETIVPELLP RLGFAARIFQ RYAVETLEFE IQPMCPANTG GGYVAGFLPD PTDSDHTFDA IQATRGAVVA KWWESRTIRP Q YARALLWT SVGKEQRLTS PGRLILLCVG NNTDVVNVSV LCRWSVRLSV PSLETPEDTF APILTLGPLY NDSLAANDFK SI LLGSTQL DIAPEGAVYS LDRPLSIDYN LGTGDVDRAV YWHVKKVAGN AGTPAGWFHW GLWDNFNKTF TQGTAYYSDA QPR QILLPV GTLFTRADSG N

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.9 mg/mL
BufferpH: 7.2
Details: PBS (140 mM NaCl, 15 mM KH2PO4, 80 mM Na2HPO4, 27 mM KCl, pH 7.2)
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 281 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 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 real images: 2359 / Average exposure time: 2.0 sec. / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 20887
CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: Low resolution cryo-EM map generated in-house.
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0)
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 2.0)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 16616
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4wiz

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 137 / Target criteria: Cross-correlation coefficient
Output model

PDB-6rj0:
Atlantic Cod Nervous Necrosis Virus-Like Particle produced in Nicotiana benthamiana

+
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