[English] 日本語
Yorodumi
- EMDB-0298: Virus-like Particles based on Potato Virus Y -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0298
TitleVirus-like Particles based on Potato Virus Y
Map dataCryoEM map of Virus-Like Particle from Potato virus Y
Sample
  • Complex: Virus-like Particle based on Potato Virus Y
    • Complex: Coat protein of Potato Virus Y
      • Protein or peptide: PolyproteinProteolysis
Function / homology
Function and homology information


nuclear-inclusion-a endopeptidase / helper-component proteinase / RNA-protein covalent cross-linking / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / helical viral capsid / serine-type peptidase activity / membrane => GO:0016020 / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity ...nuclear-inclusion-a endopeptidase / helper-component proteinase / RNA-protein covalent cross-linking / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / helical viral capsid / serine-type peptidase activity / membrane => GO:0016020 / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / RNA binding / ATP binding
Similarity search - Function
Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Potyvirus P1 protease / Potyviridae polyprotein / Protein P3 of Potyviral polyprotein ...Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Potyvirus P1 protease / Potyviridae polyprotein / Protein P3 of Potyviral polyprotein / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain profile. / Potyviridae P1 protease domain profile. / Potyvirus NIa protease (NIa-pro) domain / Peptidase family C4 / Potyvirus NIa protease (NIa-pro) domain profile. / Potyvirus coat protein / Potyvirus coat protein / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesPotato virus Y
Methodhelical reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsPodobnik M / Kezar A / Novacek J
Funding support Slovenia, Czech Republic, 3 items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0391 Slovenia
Ministry of Education, Youth and Sports of the Czech RepublicLM2015043 Czech Republic
Slovenian Research AgencyJ7-7248 Slovenia
CitationJournal: Sci Adv / Year: 2019
Title: Structural basis for the multitasking nature of the potato virus Y coat protein.
Authors: Andreja Kežar / Luka Kavčič / Martin Polák / Jiří Nováček / Ion Gutiérrez-Aguirre / Magda Tušek Žnidarič / Anna Coll / Katja Stare / Kristina Gruden / Maja Ravnikar / David ...Authors: Andreja Kežar / Luka Kavčič / Martin Polák / Jiří Nováček / Ion Gutiérrez-Aguirre / Magda Tušek Žnidarič / Anna Coll / Katja Stare / Kristina Gruden / Maja Ravnikar / David Pahovnik / Ema Žagar / Franci Merzel / Gregor Anderluh / Marjetka Podobnik /
Abstract: Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near-atomic structure of PVY's flexuous virions, revealing a previously ...Potato virus Y (PVY) is among the most economically important plant pathogens. Using cryoelectron microscopy, we determined the near-atomic structure of PVY's flexuous virions, revealing a previously unknown lumenal interplay between extended carboxyl-terminal regions of the coat protein units and viral RNA. RNA-coat protein interactions are crucial for the helical configuration and stability of the virion, as revealed by the unique near-atomic structure of RNA-free virus-like particles. The structures offer the first evidence for plasticity of the coat protein's amino- and carboxyl-terminal regions. Together with mutational analysis and in planta experiments, we show their crucial role in PVY infectivity and explain the ability of the coat protein to perform multiple biological tasks. Moreover, the high modularity of PVY virus-like particles suggests their potential as a new molecular scaffold for nanobiotechnological applications.
History
DepositionOct 18, 2018-
Header (metadata) releaseNov 14, 2018-
Map releaseAug 7, 2019-
UpdateAug 7, 2019-
Current statusAug 7, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6hxz
  • Surface level: 1.25
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6hxz
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0298.png

Downloads & links

-
Map

FileDownload / File: emd_0298.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of Virus-Like Particle from Potato virus Y
Voxel sizeX=Y=Z: 1.061 Å
Density
Contour LevelBy AUTHOR: 1.25 / Movie #1: 1.25
Minimum - Maximum-6.7585998 - 9.995189999999999
Average (Standard dev.)0.00027839007 (±0.353567)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0611.0611.061
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z381.960381.960381.960
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-6.7599.9950.000

-
Supplemental data

-
Half map: Second half-map after 3D auto-refine in Relion.

Fileemd_0298_half_map_1.map
AnnotationSecond half-map after 3D auto-refine in Relion.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: First half-map after 3D auto-refine in Relion.

Fileemd_0298_half_map_2.map
AnnotationFirst half-map after 3D auto-refine in Relion.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Virus-like Particle based on Potato Virus Y

EntireName: Virus-like Particle based on Potato Virus Y
Components
  • Complex: Virus-like Particle based on Potato Virus Y
    • Complex: Coat protein of Potato Virus Y
      • Protein or peptide: PolyproteinProteolysis

-
Supramolecule #1: Virus-like Particle based on Potato Virus Y

SupramoleculeName: Virus-like Particle based on Potato Virus Y / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Recombinantly expressed coat protein self-assembles into virus-like particles.
Source (natural)Organism: Potato virus Y / Strain: NTN
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) / Recombinant plasmid: pT7-7

-
Supramolecule #2: Coat protein of Potato Virus Y

SupramoleculeName: Coat protein of Potato Virus Y / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Potato virus Y / Strain: NTN
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21(DE3) / Recombinant plasmid: pT7-7
Molecular weightTheoretical: 299 KDa

-
Macromolecule #1: Polyprotein

MacromoleculeName: Polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Potato virus Y
Molecular weightTheoretical: 29.935797 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTSG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQ FDTWYEAVQL AYDIGETEMP TVMNGLMVWC IENGTSPNIN GVWVMMDGDE QVEYPLKPIV ENAKPTLRQI M AHFSDVAE ...String:
GNDTIDAGGS TKKDAKQEQG SIQPNLNKEK EKDVNVGTSG THTVPRIKAI TSKMRMPKSK GATVLNLEHL LEYAPQQIDI SNTRATQSQ FDTWYEAVQL AYDIGETEMP TVMNGLMVWC IENGTSPNIN GVWVMMDGDE QVEYPLKPIV ENAKPTLRQI M AHFSDVAE AYIEMRNKKE PYMPRYGLVR NLRDGSLARY AFDFYEVTSR TPVRAREAHI QMKAAALKSA QSRLFGLDGG IS TQEENTE RHTTEDVSPS MHTLLGVKNM

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration6.7 mg/mL
BufferpH: 7.4 / Component - Concentration: 12.0 mM / Component - Formula: PBS / Component - Name: Phosphate buffered saline / Details: 140 mM NaCl 2.7 mM KCl
GridModel: Quantifoil R2/1 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-16 / Number real images: 5344 / Average electron dose: 48.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Segment selectionNumber selected: 244988 / Software - Name: EMAN2 / Software - details: e2helixboxer.py
CTF correctionSoftware - Name: Gctf (ver. 1.05)
Startup modelType of model: INSILICO MODEL
In silico model: Featureless cylinder constructed in Relion.
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 42.65 Å
Applied symmetry - Helical parameters - Δ&Phi: 13.24 °
Applied symmetry - Helical parameters - Axial symmetry: C8 (8 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 148876
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