6OLA

Structure of the PCV2d virus-like particle

  • Classification: VIRUS LIKE PARTICLE
  • Organism(s): Porcine circovirus 2
  • Expression System: Homo sapiens

  • 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; National Institutes of Health/National Institute on Minority Health and Health Disparities; National Institutes of Health/National Institute of General Medical Sciences 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 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

  • 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 ...

    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

    Department of Physics, City College of New York, New York, NY, 10031, USA.,Department of Chemistry and Biochemistry, The City College of New York, New York, NY, 10031, USA; Graduate Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY, 10016, USA. Electronic address: rkhayat@ccny.cuny.edu.,CUNY School of Medicine, City College of New York, NY, 10031, USA.,TechnoVax, Inc., 6 Westchester Plaza, Elmsford, NY, 10523, USA.,Biologics Development, Huvepharma, 3A Nikolay Haytov Street, Sofia, 1113, Bulgaria.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Capsid protein
A0, A1, A2, A3, A4, A5, A6, A7, A8, A9, AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM, AN, AO, AP, AQ, AR, AS, AT, AU, AV, AW, AX, AY, AZ, Aa, Ab, Ac, Ad, Ae, Af, Ag, Ah, Ai, Aj, Ak, Al, Am, An, Ao, Ap, Aq, Ar, As, At, Au, Av, Aw, Ax
196Porcine circovirus 2Mutation(s): 0 
Gene Names: ORF2
Find proteins for G0ZPI6 (Porcine circovirus 2)
Go to UniProtKB:  G0ZPI6
Entity ID: 2
MoleculeChainsLengthOrganism
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: 3.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited States5SC1AI114843
National Institutes of Health/National Institute on Minority Health and Health DisparitiesUnited States5G12MD007603
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM103310

Revision History 

  • Version 1.0: 2019-09-25
    Type: Initial release