[English] 日本語
Yorodumi
- EMDB-17046: Virus-like Particle based on PVY coat protein with stacked-ring a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17046
TitleVirus-like Particle based on PVY coat protein with stacked-ring architecture
Map dataVLPr sharp symmetric cryoEM map (C8)
Sample
  • Complex: Virus-like particle from PVY coat protein
    • Protein or peptide: Genome polyprotein (Fragment)
Keywordsstacked-ring / VLP / Potyvirus / PVY / VIRUS LIKE PARTICLE
Function / homologyPotyvirus coat protein / Potyvirus coat protein / viral capsid / Genome polyprotein
Function and homology information
Biological speciesPotato virus Y strain NTN
Methodhelical reconstruction / cryo EM / Resolution: 3.34 Å
AuthorsKavcic L / Kezar A / Podobnik M
Funding support Slovenia, 2 items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0391 Slovenia
Slovenian Research AgencyJ7-7248 Slovenia
CitationJournal: Commun Chem / Year: 2024
Title: From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y.
Authors: Luka Kavčič / Andreja Kežar / Neža Koritnik / Magda Tušek Žnidarič / Tajda Klobučar / Žiga Vičič / Franci Merzel / Ellie Holden / Justin L P Benesch / Marjetka Podobnik /
Abstract: The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid ...The structural diversity and tunability of the capsid proteins (CPs) of various icosahedral and rod-shaped viruses have been well studied and exploited in the development of smart hybrid nanoparticles. However, the potential of CPs of the wide-spread flexuous filamentous plant viruses remains to be explored. Here, we show that we can control the shape, size, RNA encapsidation ability, symmetry, stability and surface functionalization of nanoparticles through structure-based design of CP from potato virus Y (PVY). We provide high-resolution insight into CP-based self-assemblies, ranging from large polymorphic or monomorphic filaments to smaller annular, cubic or spherical particles. Furthermore, we show that we can prevent CP self-assembly in bacteria by fusion with a cleavable protein, enabling controlled nanoparticle formation in vitro. Understanding the remarkable structural diversity of PVY CP not only provides possibilities for the production of biodegradable nanoparticles, but may also advance future studies of CP's polymorphism in a biological context.
History
DepositionApr 7, 2023-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17046.png

Downloads & links

-
Map

FileDownload / File: emd_17046.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVLPr sharp symmetric cryoEM map (C8)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å		0.95 Å/pix.
x 300 pix.
= 285. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.519
Minimum - Maximum-2.052845 - 3.8674426
Average (Standard dev.)0.0194004 (±0.17609921)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 285.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_17046_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: VLPr raw cryoEM map (C8)

Fileemd_17046_additional_1.map
AnnotationVLPr raw cryoEM map (C8)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: VLPr half B cryoEM map

Fileemd_17046_half_map_1.map
AnnotationVLPr half B cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: VLPr half A cryoEM map

Fileemd_17046_half_map_2.map
AnnotationVLPr half A cryoEM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Virus-like particle from PVY coat protein

EntireName: Virus-like particle from PVY coat protein
Components
  • Complex: Virus-like particle from PVY coat protein
    • Protein or peptide: Genome polyprotein (Fragment)

-
Supramolecule #1: Virus-like particle from PVY coat protein

SupramoleculeName: Virus-like particle from PVY coat protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: The sample contains 3 forms of filaments.
Source (natural)Organism: Potato virus Y strain NTN

-
Macromolecule #1: Genome polyprotein (Fragment)

MacromoleculeName: Genome polyprotein (Fragment) / type: protein_or_peptide / ID: 1
Details: Due to flexibility, structural model could only be built from H42 to A222.
Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Potato virus Y strain NTN / Strain: NTN
Molecular weightTheoretical: 29.935797 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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

UniProtKB: Genome polyprotein

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
Details: 1.8 mM KH2PO4, 10.1 mM Na2HPO4, 140 mM NaCl, 2.7 mM KCl, pH 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 502 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 150000
Sample stageCooling holder cryogen: NITROGEN

+
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 43.244 Å
Applied symmetry - Helical parameters - Δ&Phi: 13.783 °
Applied symmetry - Helical parameters - Axial symmetry: C8 (8 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1)
Details: cryoSPARC Helical refinement with initial helical parameters from EMD-0298
Number images used: 49140
Segment selectionNumber selected: 109796 / Software - Name: cryoSPARC (ver. 3.3) / Software - details: Filament tracer / Details: cryosparc filament tracer
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6hxz


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8opa:
Virus-like Particle based on PVY coat protein with stacked-ring architecture

+
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