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- PDB-6ola: Structure of the PCV2d virus-like particle -

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Basic information

Entry
Database: PDB / ID: 6ola
TitleStructure of the PCV2d virus-like particle
Components
  • Capsid protein
  • DNA (5'-D(P*CP*CP*GP*G)-3')
KeywordsVIRUS LIKE PARTICLE / Circovirus / viral jelly roll
Function / homology
Function and homology information


viral capsid assembly / T=1 icosahedral viral capsid / viral penetration into host nucleus / host cell / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus
Similarity search - Function
Circovirus capsid protein / Circovirus capsid superfamily / Circovirus capsid protein
Similarity search - Domain/homology
DNA / Capsid protein
Similarity search - Component
Biological speciesPorcine circovirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKhayat, R. / Wen, K. / Alimova, A. / Galarza, J. / Gottlieb, P.
Funding support United States, 3items
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, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A0: Capsid protein
A1: Capsid protein
A2: Capsid protein
A3: Capsid protein
A4: Capsid protein
A5: Capsid protein
A6: Capsid protein
A7: Capsid protein
A8: Capsid protein
A9: Capsid protein
AA: Capsid protein
AB: Capsid protein
AC: Capsid protein
AD: Capsid protein
AE: Capsid protein
AF: Capsid protein
AG: Capsid protein
AH: Capsid protein
AI: Capsid protein
AJ: Capsid protein
AK: Capsid protein
AL: Capsid protein
AM: Capsid protein
AN: Capsid protein
AO: Capsid protein
AP: Capsid protein
AQ: Capsid protein
AR: Capsid protein
AS: Capsid protein
AT: Capsid protein
AU: Capsid protein
AV: Capsid protein
AW: Capsid protein
AX: Capsid protein
AY: Capsid protein
AZ: Capsid protein
Aa: Capsid protein
Ab: Capsid protein
Ac: Capsid protein
Ad: Capsid protein
Ae: Capsid protein
Af: Capsid protein
Ag: Capsid protein
Ah: Capsid protein
Ai: Capsid protein
Aj: Capsid protein
Ak: Capsid protein
Al: Capsid protein
Am: Capsid protein
An: Capsid protein
Ao: Capsid protein
Ap: Capsid protein
Aq: Capsid protein
Ar: Capsid protein
As: Capsid protein
At: Capsid protein
Au: Capsid protein
Av: Capsid protein
Aw: Capsid protein
Ax: Capsid protein
B0: DNA (5'-D(P*CP*CP*GP*G)-3')
B1: DNA (5'-D(P*CP*CP*GP*G)-3')
B2: DNA (5'-D(P*CP*CP*GP*G)-3')
B3: DNA (5'-D(P*CP*CP*GP*G)-3')
B4: DNA (5'-D(P*CP*CP*GP*G)-3')
B5: DNA (5'-D(P*CP*CP*GP*G)-3')
B6: DNA (5'-D(P*CP*CP*GP*G)-3')
B7: DNA (5'-D(P*CP*CP*GP*G)-3')
B8: DNA (5'-D(P*CP*CP*GP*G)-3')
B9: DNA (5'-D(P*CP*CP*GP*G)-3')
BA: DNA (5'-D(P*CP*CP*GP*G)-3')
BB: DNA (5'-D(P*CP*CP*GP*G)-3')
BC: DNA (5'-D(P*CP*CP*GP*G)-3')
BD: DNA (5'-D(P*CP*CP*GP*G)-3')
BE: DNA (5'-D(P*CP*CP*GP*G)-3')
BF: DNA (5'-D(P*CP*CP*GP*G)-3')
BG: DNA (5'-D(P*CP*CP*GP*G)-3')
BH: DNA (5'-D(P*CP*CP*GP*G)-3')
BI: DNA (5'-D(P*CP*CP*GP*G)-3')
BJ: DNA (5'-D(P*CP*CP*GP*G)-3')
BK: DNA (5'-D(P*CP*CP*GP*G)-3')
BL: DNA (5'-D(P*CP*CP*GP*G)-3')
BM: DNA (5'-D(P*CP*CP*GP*G)-3')
BN: DNA (5'-D(P*CP*CP*GP*G)-3')
BO: DNA (5'-D(P*CP*CP*GP*G)-3')
BP: DNA (5'-D(P*CP*CP*GP*G)-3')
BQ: DNA (5'-D(P*CP*CP*GP*G)-3')
BR: DNA (5'-D(P*CP*CP*GP*G)-3')
BS: DNA (5'-D(P*CP*CP*GP*G)-3')
BT: DNA (5'-D(P*CP*CP*GP*G)-3')
BU: DNA (5'-D(P*CP*CP*GP*G)-3')
BV: DNA (5'-D(P*CP*CP*GP*G)-3')
BW: DNA (5'-D(P*CP*CP*GP*G)-3')
BX: DNA (5'-D(P*CP*CP*GP*G)-3')
BY: DNA (5'-D(P*CP*CP*GP*G)-3')
BZ: DNA (5'-D(P*CP*CP*GP*G)-3')
Ba: DNA (5'-D(P*CP*CP*GP*G)-3')
Bb: DNA (5'-D(P*CP*CP*GP*G)-3')
Bc: DNA (5'-D(P*CP*CP*GP*G)-3')
Bd: DNA (5'-D(P*CP*CP*GP*G)-3')
Be: DNA (5'-D(P*CP*CP*GP*G)-3')
Bf: DNA (5'-D(P*CP*CP*GP*G)-3')
Bg: DNA (5'-D(P*CP*CP*GP*G)-3')
Bh: DNA (5'-D(P*CP*CP*GP*G)-3')
Bi: DNA (5'-D(P*CP*CP*GP*G)-3')
Bj: DNA (5'-D(P*CP*CP*GP*G)-3')
Bk: DNA (5'-D(P*CP*CP*GP*G)-3')
Bl: DNA (5'-D(P*CP*CP*GP*G)-3')
Bm: DNA (5'-D(P*CP*CP*GP*G)-3')
Bn: DNA (5'-D(P*CP*CP*GP*G)-3')
Bo: DNA (5'-D(P*CP*CP*GP*G)-3')
Bp: DNA (5'-D(P*CP*CP*GP*G)-3')
Bq: DNA (5'-D(P*CP*CP*GP*G)-3')
Br: DNA (5'-D(P*CP*CP*GP*G)-3')
Bs: DNA (5'-D(P*CP*CP*GP*G)-3')
Bt: DNA (5'-D(P*CP*CP*GP*G)-3')
Bu: DNA (5'-D(P*CP*CP*GP*G)-3')
Bv: DNA (5'-D(P*CP*CP*GP*G)-3')
Bw: DNA (5'-D(P*CP*CP*GP*G)-3')
Bx: DNA (5'-D(P*CP*CP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)1,455,713120
Polymers1,455,713120
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Capsid protein / Putative capsid protein


Mass: 23070.059 Da / Num. of mol.: 60 / Fragment: UNP residues 36-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine circovirus 2 / Gene: ORF2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: G0ZPI6
#2: DNA chain ...
DNA (5'-D(P*CP*CP*GP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine circovirus 2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Porcine circovirus 2 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Porcine circovirus 2
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 64 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: Leginon / Category: image acquisition
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4442 / Symmetry type: POINT

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