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- EMDB-20113: Structure of the PCV2d virus-like particle -

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Basic information

Entry
Database: EMDB / ID: EMD-20113
TitleStructure of the PCV2d virus-like particle
Map dataPCV2d virus-like particle
Sample
  • Virus: Porcine circovirus 2
    • Protein or peptide: Capsid protein
    • DNA: DNA (5'-D(P*CP*CP*GP*G)-3')
KeywordsCircovirus / viral jelly roll / VIRUS LIKE PARTICLE
Function / homologyCircovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein / viral capsid assembly / T=1 icosahedral viral capsid / symbiont entry into host cell / virion attachment to host cell / Capsid protein
Function and homology information
Biological speciesPorcine circovirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKhayat R / Wen K
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5SC1AI114843 United States
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)5G12MD007603 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
CitationJournal: Virology / Year: 2019
Title: Structural characterization of the PCV2d virus-like particle at 3.3 Å resolution reveals differences to PCV2a and PCV2b capsids, a tetranucleotide, and an N-terminus near the icosahedral 3-fold axes.
Authors: Reza Khayat / Ke Wen / Aleksandra Alimova / Boris Gavrilov / Al Katz / Jose M Galarza / Paul Gottlieb /
Abstract: Porcine circovirus 2 (PCV2) has a major impact on the swine industry. Eight PCV2 genotypes (a-h) have been identified using capsid sequence analysis. PCV2d has been designated as the emerging ...Porcine circovirus 2 (PCV2) has a major impact on the swine industry. Eight PCV2 genotypes (a-h) have been identified using capsid sequence analysis. PCV2d has been designated as the emerging genotype. The cryo-electron microscopy molecular envelope of PCV2d virus-like particles identifies differences between PCV2a, b and d genotypes that accompany the emergence of PCV2b from PCV2a, and PCV2d from PCV2b. These differences indicate that sequence analysis of genotypes is insufficient, and that it is important to determine the PCV2 capsid structure as the virus evolves. Structure-based sequence comparison demonstrate that each genotype possesses a unique combination of amino acids located on the surface of the capsid that undergo substitution. We also demonstrate that the capsid N-terminus moves in response to increasing amount of nucleic acid packaged into the capsid. Furthermore, we model a tetranucleotide between the 5- and 2-fold axes of symmetry that appears to be responsible for capsid stability.
History
DepositionApr 16, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseSep 25, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ola
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ola
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20113.png

Downloads & links

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Map

FileDownload / File: emd_20113.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPCV2d virus-like particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.04049722 - 0.12216126
Average (Standard dev.)0.0028415734 (±0.009130166)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z324.000324.000324.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0400.1220.003

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Supplemental data

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Sample components

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Entire : Porcine circovirus 2

EntireName: Porcine circovirus 2
Components
  • Virus: Porcine circovirus 2
    • Protein or peptide: Capsid protein
    • DNA: DNA (5'-D(P*CP*CP*GP*G)-3')

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Supramolecule #1: Porcine circovirus 2

SupramoleculeName: Porcine circovirus 2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 85708 / Sci species name: Porcine circovirus 2 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Porcine circovirus 2
Molecular weightTheoretical: 23.070059 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YRWRRKNGIF NTRLSRTIGY TVKKTTVRTP SWNVDMMRFN INDFLPPGGG SNPLTVPFEY YRIRKVKVEF WPCSPITQGD RGVGSTAVI LDDNFVTKAN ALTYDPYVNY SSRHTITQPF SYHSRYFTPK PVLDRTIDYF QPNNKRNQLW LRLQTTGNVD H VGLGTAFE ...String:
YRWRRKNGIF NTRLSRTIGY TVKKTTVRTP SWNVDMMRFN INDFLPPGGG SNPLTVPFEY YRIRKVKVEF WPCSPITQGD RGVGSTAVI LDDNFVTKAN ALTYDPYVNY SSRHTITQPF SYHSRYFTPK PVLDRTIDYF QPNNKRNQLW LRLQTTGNVD H VGLGTAFE NSIYDQDYNI RITMYVQFRE FNLKDPPL

UniProtKB: Capsid protein

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Macromolecule #2: DNA (5'-D(P*CP*CP*GP*G)-3')

MacromoleculeName: DNA (5'-D(P*CP*CP*GP*G)-3') / type: dna / ID: 2 / Number of copies: 60 / Classification: DNA
Source (natural)Organism: Porcine circovirus 2
Molecular weightTheoretical: 1.191818 KDa
SequenceString:
(DC)(DC)(DG)(DG)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 64.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4442
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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