6OLA

Structure of the PCV2d virus-like particle

  • Classification: VIRUS LIKE PARTICLE
  • Organism(s): Porcine circovirus 2
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2019-04-16 Released: 2019-09-25 
  • Deposition Author(s): Khayat, R., Wen, K., Alimova, A., Galarza, J., Gottlieb, P.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural characterization of the PCV2d virus-like particle at 3.3 angstrom resolution reveals differences to PCV2a and PCV2b capsids, a tetranucleotide, and an N-terminus near the icosahedral 3-fold axes.

Khayat, R.Wen, K.Alimova, A.Gavrilov, B.Katz, A.Galarza, J.M.Gottlieb, P.

(2019) Virology 537: 186-197

  • DOI: 10.1016/j.virol.2019.09.001
  • Primary Citation of Related Structures:  
    6OLA

  • PubMed 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 genotype. The cryo-electron microscopy molecular envelope of P ...

    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.


    Organizational Affiliation

    CUNY School of Medicine, City College of New York, NY, 10031, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Capsid proteinA0A1A2A3A4A5A6A7A0A1A2A3A4A5A6A7A8A9AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZAaAbAcAdAeAfAgAhAiAjAkAlAmAnAoApAqArAsAtAuAvAwAx
196Porcine circovirus 2Mutation(s): 0 
Gene Names: ORF2
Find proteins for G0ZPI6 (Porcine circovirus 2)
Explore G0ZPI6 
Go to UniProtKB:  G0ZPI6
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*CP*CP*GP*G)-3')B0, B1, B2, B3, B4, B5, B6, B7, B8, B9, BA, BB, BC, BD, BE, BF, BG, BH, BI, BJ, BK, BL, BM, BN, BO, BP, BQ, BR, BS, BT, BU, BV, BW, BX, BY, BZ, Ba, Bb, Bc, Bd, Be, Bf, Bg, Bh, Bi, Bj, Bk, Bl, Bm, Bn, Bo, Bp, Bq, Br, Bs, Bt, Bu, Bv, Bw, Bx4Porcine circovirus 2
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.30 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States5SC1AI114843
    National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)United States5G12MD007603
    National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103310

    Revision History 

    • Version 1.0: 2019-09-25
      Type: Initial release
    • Version 1.1: 2019-12-18
      Changes: Author supporting evidence